1-8958967-C-A

Variant names:

• chr1-8958967-C-A
• NM_001215.4:c.466C>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001215.4(CA6):​c.466C>A​(p.Pro156Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P156L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CA6 NM_001215.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.844

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28703606).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA6	NM_001215.4	c.466C>A	p.Pro156Thr	missense_variant	Exon 4 of 8	ENST00000377443.7	NP_001206.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA6	ENST00000377443.7	c.466C>A	p.Pro156Thr	missense_variant	Exon 4 of 8	1	NM_001215.4	ENSP00000366662.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 03, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.466C>A (p.P156T) alteration is located in exon 4 (coding exon 4) of the CA6 gene. This alteration results from a C to A substitution at nucleotide position 466, causing the proline (P) at amino acid position 156 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.36	.;T;.;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.067	N
LIST_S2	Uncertain	0.88	D;T;T;D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.29	T;T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Uncertain	2.7	.;M;M;.
PrimateAI	Benign	0.35	T
PROVEAN	Pathogenic	-5.9	D;D;D;D
REVEL	Benign	0.12
Sift	Uncertain	0.0050	D;D;D;D
Sift4G	Uncertain	0.019	D;D;D;D
Polyphen		0.92	.;P;.;.
Vest4		0.26, 0.26
MutPred		0.51		.;Loss of stability (P = 0.0713);Loss of stability (P = 0.0713);.;
MVP		0.58
MPC		0.44
ClinPred		0.84	D
GERP RS		1.0
Varity_R		0.37
gMVP		0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-9019026;