rs2274330
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001215.4(CA6):āc.228G>Cā(p.Gly76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,609,944 control chromosomes in the GnomAD database, including 20,427 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.22 ( 5920 hom., cov: 32)
Exomes š: 0.12 ( 14507 hom. )
Consequence
CA6
NM_001215.4 synonymous
NM_001215.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.905
Genes affected
CA6 (HGNC:1380): (carbonic anhydrase 6) The protein encoded by this gene is one of several isozymes of carbonic anhydrase. This protein is found only in salivary glands and saliva and protein may play a role in the reversible hydratation of carbon dioxide though its function in saliva is unknown. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
?
Synonymous conserved (PhyloP=-0.905 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CA6 | NM_001215.4 | c.228G>C | p.Gly76= | synonymous_variant | 2/8 | ENST00000377443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA6 | ENST00000377443.7 | c.228G>C | p.Gly76= | synonymous_variant | 2/8 | 1 | NM_001215.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33097AN: 151900Hom.: 5893 Cov.: 32
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GnomAD3 exomes AF: 0.138 AC: 34419AN: 249508Hom.: 3778 AF XY: 0.134 AC XY: 18147AN XY: 135042
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GnomAD4 exome AF: 0.123 AC: 179793AN: 1457926Hom.: 14507 Cov.: 33 AF XY: 0.124 AC XY: 89697AN XY: 725446
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GnomAD4 genome ? AF: 0.218 AC: 33171AN: 152018Hom.: 5920 Cov.: 32 AF XY: 0.214 AC XY: 15942AN XY: 74336
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at