chr17-52000253-G-T

Variant names:

• chr17-52000253-G-T
• rs996379
• NM_020178.5:c.137-69121C>A

Variant summary

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

The NM_020178.5(CA10):​c.137-69121C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,982 control chromosomes in the GnomAD database, including 10,416 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 0.34 (10416 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA10	NM_020178.5	c.137-69121C>A		intron_variant	Intron 2 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.137-69121C>A		intron_variant	Intron 3 of 9		NP_001076002.1
CA10	NM_001082534.2	c.137-69121C>A		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.137-69121C>A		intron_variant	Intron 2 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51321 AN: 151864 Hom.: 10409 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.338 AC: 51347 AN: 151982 Hom.: 10416 Cov.: 32 AF XY: 0.345 AC XY: 25606 AN XY: 74274

African (AFR) AF: 0.128 AC: 5333 AN: 41510

American (AMR) AF: 0.499 AC: 7602 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3758 AN: 5106

South Asian (SAS) AF: 0.510 AC: 2461 AN: 4826

European-Finnish (FIN) AF: 0.352 AC: 3723 AN: 10584

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26040 AN: 67926

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.369 Hom.: 2024

Bravo AF: 0.342

Asia WGS AF: 0.571 AC: 1982 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.63
PhyloP100		-0.12
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: rs996379; hg19: chr17-50077613;