17-51882949-T-C

Position:

• chr17-51882949-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020178.5(CA10):​c.279+48041A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,026 control chromosomes in the GnomAD database, including 11,625 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: 𝑓 0.35 (11625 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

CA10 (HGNC:1369): (carbonic anhydrase 10) This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CA10	NM_020178.5	c.279+48041A>G		intron_variant		ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.279+48041A>G		intron_variant			NP_001076002.1
CA10	NM_001082534.2	c.279+48041A>G		intron_variant			NP_001076003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CA10	ENST00000451037.7	c.279+48041A>G		intron_variant		1	NM_020178.5	ENSP00000405388	P1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52916 AN: 151908 Hom.: 11629 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.348 AC: 52907 AN: 152026 Hom.: 11625 Cov.: 32 AF XY: 0.346 AC XY: 25690 AN XY: 74302

Gnomad4 AFR AF: 0.0884

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.392

Alfa AF: 0.439 Hom.: 8158

Bravo AF: 0.324

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.91

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

LitVar

Other links and lift over

dbSNP: rs967676; hg19: chr17-49960309; COSMIC: COSV53369345;