rs11079992

Positions:

• chr17-52140177-G-A

Variant summary

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

The NM_020178.5(CA10):​c.61+17549C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,998 control chromosomes in the GnomAD database, including 23,073 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 0.52 (23073 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA10	NM_020178.5	c.61+17549C>T		intron_variant		ENST00000451037.7
CA10	NM_001082533.1	c.61+17549C>T		intron_variant
CA10	NM_001082534.2	c.61+17549C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA10	ENST00000451037.7	c.61+17549C>T		intron_variant		1	NM_020178.5	P1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78298 AN: 151880 Hom.: 23016 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.516 AC: 78419 AN: 151998 Hom.: 23073 Cov.: 32 AF XY: 0.515 AC XY: 38295 AN XY: 74304

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.466

Alfa AF: 0.421 Hom.: 9022

Bravo AF: 0.528

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.013
DANN	Benign	0.42

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: rs11079992; hg19: chr17-50217537;