chr15-63328338-CT-C

Position:

• chr15-63328338-CT-C

Variant summary

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

The NM_001218.5(CA12):​c.875-209del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 140,272 control chromosomes in the GnomAD database, including 262 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.072 (262 hom., cov: 24)
• Consequence: CA12 NM_001218.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.770

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 15-63328338-CT-C is Benign according to our data. Variant chr15-63328338-CT-C is described in ClinVar as [Benign]. Clinvar id is 1245197.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CA12	NM_001218.5	c.875-209del		intron_variant		ENST00000178638.8	NP_001209.1
LOC124903506	XR_007064676.1	n.767+9600del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CA12	ENST00000178638.8	c.875-209del		intron_variant		1	NM_001218.5	ENSP00000178638	A1
CA12	ENST00000344366.7	c.875-1106del		intron_variant		1		ENSP00000343088	P4
CA12	ENST00000422263.2	c.695-1106del		intron_variant		2		ENSP00000403028
CA12	ENST00000560666.1	n.118-1106del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10143 AN: 140258 Hom.: 263 Cov.: 24

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.0609

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0925

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0724 AC: 10152 AN: 140272 Hom.: 262 Cov.: 24 AF XY: 0.0706 AC XY: 4773 AN XY: 67650

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.0755

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

Jun 18, 2021

- -

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: rs57210378; hg19: chr15-63620537;