rs203076

Variant names:

• chr17-51922125-C-A
• rs203076
• NM_020178.5:c.279+8865G>T

Variant summary

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

The NM_020178.5(CA10):​c.279+8865G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,050 control chromosomes in the GnomAD database, including 42,402 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 0.74 (42402 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA10	NM_020178.5	c.279+8865G>T		intron_variant	Intron 3 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.279+8865G>T		intron_variant	Intron 4 of 9		NP_001076002.1
CA10	NM_001082534.2	c.279+8865G>T		intron_variant	Intron 4 of 9		NP_001076003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CA10	ENST00000451037.7	c.279+8865G>T		intron_variant	Intron 3 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112938 AN: 151932 Hom.: 42380 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.743 AC: 113012 AN: 152050 Hom.: 42402 Cov.: 32 AF XY: 0.738 AC XY: 54848 AN XY: 74306

African (AFR) AF: 0.804 AC: 33367 AN: 41502

American (AMR) AF: 0.676 AC: 10309 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2705 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2638 AN: 5156

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4816

European-Finnish (FIN) AF: 0.732 AC: 7739 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50311 AN: 67958

Other (OTH) AF: 0.740 AC: 1562 AN: 2112

Alfa AF: 0.733 Hom.: 19570

Bravo AF: 0.737

Asia WGS AF: 0.639 AC: 2224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.68
DANN	Benign	0.55
PhyloP100		0.066
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: rs203076; hg19: chr17-49999485;