rs1392935

Variant names:

• chr17-51861769-G-A
• rs1392935
• NM_020178.5:c.279+69221C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020178.5(CA10):​c.279+69221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,070 control chromosomes in the GnomAD database, including 3,579 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 0.17 (3579 hom., cov: 32)
• Consequence: CA10 NM_020178.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CA10	NM_020178.5	c.279+69221C>T		intron_variant	Intron 3 of 8	ENST00000451037.7	NP_064563.1
CA10	NM_001082533.1	c.279+69221C>T		intron_variant	Intron 4 of 9		NP_001076002.1
CA10	NM_001082534.2	c.279+69221C>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+69221C>T		intron_variant	Intron 3 of 8	1	NM_020178.5	ENSP00000405388.2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25810 AN: 151952 Hom.: 3565 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.170 AC: 25870 AN: 152070 Hom.: 3579 Cov.: 32 AF XY: 0.166 AC XY: 12359 AN XY: 74320

African (AFR) AF: 0.391 AC: 16214 AN: 41448

American (AMR) AF: 0.104 AC: 1586 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3472

East Asian (EAS) AF: 0.0242 AC: 125 AN: 5172

South Asian (SAS) AF: 0.105 AC: 505 AN: 4824

European-Finnish (FIN) AF: 0.0705 AC: 746 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5973 AN: 67992

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.156 Hom.: 496

Bravo AF: 0.183

Asia WGS AF: 0.104 AC: 359 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.59
PhyloP100		2.4
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: rs1392935; hg19: chr17-49939129;