NM_020178.5:c.137-4785C>A

Variant names:

• chr17-51935917-G-T
• rs203097
• NM_020178.5:c.137-4785C>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.137-4785C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,034 control chromosomes in the GnomAD database, including 35,075 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 (35075 hom., cov: 33)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 2 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=-0.93).
• 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.137-4785C>A		intron_variant	Intron 2 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.137-4785C>A		intron_variant	Intron 3 of 9		NP_001076002.1
CA10	NM_001082534.2	c.137-4785C>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.137-4785C>A		intron_variant	Intron 2 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102689 AN: 151918 Hom.: 35064 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.676 AC: 102742 AN: 152034 Hom.: 35075 Cov.: 33 AF XY: 0.671 AC XY: 49878 AN XY: 74306

African (AFR) AF: 0.640 AC: 26537 AN: 41488

American (AMR) AF: 0.634 AC: 9660 AN: 15248

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

East Asian (EAS) AF: 0.510 AC: 2620 AN: 5140

South Asian (SAS) AF: 0.648 AC: 3124 AN: 4820

European-Finnish (FIN) AF: 0.697 AC: 7382 AN: 10594

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

European-Non Finnish (NFE) AF: 0.713 AC: 48422 AN: 67954

Other (OTH) AF: 0.693 AC: 1463 AN: 2112

Alfa AF: 0.578 Hom.: 2145

Bravo AF: 0.664

Asia WGS AF: 0.576 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.71
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs203097; hg19: chr17-50013277;