[ERROR] Malformed VCF: empty alleles are not permitted in VCF records

I am running BaseRecalibrator for my RNA-seq:

java -jar -Xmx120g ${GATK} -T BaseRecalibrator -R "${reference}" -I "${file4}" -knownSites "${gerVar}" -knownSites "${somVar}" -o "${file4%_tstaids.bam}_tstaidsr.table1"
java -jar -Xmx120g ${GATK} -T BaseRecalibrator -R "${reference}" -I "${file4}" -knownSites "${gerVar}" -knownSites "${somVar}" -BQSR "${file4%_tstaids.bam}_tstaidsr.table1" -o "${file4%_tstaids.bam}_tstaidsr.table2"
java -jar -Xmx120g ${GATK} -T AnalyzeCovariates -R "${reference}" -before "${file4%_tstaids.bam}_tstaidsr.table1" -after "${file4%_tstaids.bam}_tstaidsr.table2" -plots "${file1%_tsta.bam}_BQSR.pdf"
java -jar -Xmx120g ${GATK} -T PrintReads -R "{reference}" -I "${file4}" -BQSR "${file4%_tstaids.bam}_tstaidsr.table1" -o "${file7}"

Note that I got 2 variant VCF from Ensembl (germline and somatic). My reference is Ensembl GRCh38.p5. I ran the command below to append 'chr' notation and change chrMT to chrM:

sed -e '/^[^#]/s/^/chr/' -e 's/^chrMT/chrM/'

I received this error:

##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 18354680: empty alleles are not permitted in VCF records

I used the command below to inspect my VCF file (it is ${gerVar} that is malformed):

sed -n '18354680p'

which returned:

chr11 5249456 HbVar.633 G . . PhenCode_20140430;TSA=sequence_alteration;AA=A