17-51976841-G-A

Position:

• chr17-51976841-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.137-45709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,040 control chromosomes in the GnomAD database, including 61,258 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 0.90 (61258 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA10	NM_020178.5	c.137-45709C>T		intron_variant		ENST00000451037.7
CA10	NM_001082533.1	c.137-45709C>T		intron_variant
CA10	NM_001082534.2	c.137-45709C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA10	ENST00000451037.7	c.137-45709C>T		intron_variant		1	NM_020178.5	P1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136321 AN: 151922 Hom.: 61221 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.897 AC: 136414 AN: 152040 Hom.: 61258 Cov.: 32 AF XY: 0.896 AC XY: 66611 AN XY: 74318

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.888

Alfa AF: 0.910 Hom.: 28733

Bravo AF: 0.896

Asia WGS AF: 0.875 AC: 3028 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.32

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: rs425459; hg19: chr17-50054201;