17-51934409-T-G

Variant names:

• chr17-51934409-T-G
• rs203096
• NM_020178.5:c.137-3277A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020178.5(CA10):​c.137-3277A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,928 control chromosomes in the GnomAD database, including 35,267 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 0.68 (35267 hom., cov: 31)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA10	NM_020178.5	c.137-3277A>C		intron_variant	Intron 2 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.137-3277A>C		intron_variant	Intron 3 of 9		NP_001076002.1
CA10	NM_001082534.2	c.137-3277A>C		intron_variant	Intron 3 of 9		NP_001076003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA10	ENST00000451037.7	c.137-3277A>C		intron_variant	Intron 2 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102977 AN: 151810 Hom.: 35255 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.678 AC: 103031 AN: 151928 Hom.: 35267 Cov.: 31 AF XY: 0.673 AC XY: 49992 AN XY: 74242

African (AFR) AF: 0.648 AC: 26852 AN: 41434

American (AMR) AF: 0.634 AC: 9662 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2598 AN: 3472

East Asian (EAS) AF: 0.511 AC: 2622 AN: 5136

South Asian (SAS) AF: 0.647 AC: 3112 AN: 4810

European-Finnish (FIN) AF: 0.696 AC: 7348 AN: 10562

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48433 AN: 67966

Other (OTH) AF: 0.696 AC: 1468 AN: 2110

Alfa AF: 0.680 Hom.: 4579

Bravo AF: 0.667

Asia WGS AF: 0.577 AC: 2006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.55
PhyloP100		-0.013
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs203096; hg19: chr17-50011769;