chr15-63339270-CAGAG-C

Position:

• chr15-63339270-CAGAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001218.5(CA12):​c.748-329_748-326del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 146,686 control chromosomes in the GnomAD database, including 196 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.046 (196 hom., cov: 31)
• Consequence: CA12 NM_001218.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.30

Genes affected

CA12 (HGNC:1371): (carbonic anhydrase 12) Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva, and gastric acid. This gene product is a type I membrane protein that is highly expressed in normal tissues, such as kidney, colon and pancreas, and has been found to be overexpressed in 10% of clear cell renal carcinomas. Three transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2014]

LOC124903506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-63339270-CAGAG-C is Benign according to our data. Variant chr15-63339270-CAGAG-C is described in ClinVar as [Benign]. Clinvar id is 1276183.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA12	NM_001218.5	c.748-329_748-326del		intron_variant		ENST00000178638.8
LOC124903506	XR_007064676.1	n.768-2542_768-2539del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA12	ENST00000178638.8	c.748-329_748-326del		intron_variant		1	NM_001218.5	A1
CA12	ENST00000344366.7	c.748-329_748-326del		intron_variant		1		P4
CA12	ENST00000422263.2	c.568-329_568-326del		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 6780 AN: 146574 Hom.: 196 Cov.: 31

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0611

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0645

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0462 AC: 6783 AN: 146686 Hom.: 196 Cov.: 31 AF XY: 0.0457 AC XY: 3264 AN XY: 71422

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0548

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0639

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0482 Hom.: 24

Asia WGS AF: 0.0360 AC: 126 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs750969716; hg19: chr15-63631469;