Variant chr15-63338692-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001218.5(CA12):c.874+127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 1,268,870 control chromosomes in the GnomAD database, including 2,320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.045 ( 200 hom., cov: 32)

Exomes 𝑓: 0.059 ( 2120 hom. )

Consequence

CA12
NM_001218.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44

Variant links:

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]

CA12 links:

LOC124903506 (HGNC:):

LOC124903506 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 15-63338692-C-T is Benign according to our data. Variant chr15-63338692-C-T is described in ClinVar as [Benign]. Clinvar id is 1282856.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA12	NM_001218.5 linkuse as main transcript	c.874+127G>A		intron_variant		ENST00000178638.8
LOC124903506	XR_007064676.1 linkuse as main transcript	n.768-3122C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
CA12	ENST00000178638.8 linkuse as main transcript	c.874+127G>A	intron_variant	1	NM_001218.5	A1	O43570-1
CA12	ENST00000344366.7 linkuse as main transcript	c.874+127G>A	intron_variant	1		P4	O43570-2
CA12	ENST00000422263.2 linkuse as main transcript	c.694+127G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0447

AC:

6794

AN:

152106

Hom.:

200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.0523

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.0129

Gnomad SAS

AF:

0.0502

Gnomad FIN

AF:

0.0500

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0626

Gnomad OTH

AF:

0.0513

GnomAD4 exome

AF:

0.0587

AC:

65592

AN:

1116646

Hom.:

2120

AF XY:

0.0596

AC XY:

33908

AN XY:

568522

show subpopulations

Gnomad4 AFR exome

AF:

0.00947

Gnomad4 AMR exome

AF:

0.0333

Gnomad4 ASJ exome

AF:

0.0815

Gnomad4 EAS exome

AF:

0.0178

Gnomad4 SAS exome

AF:

0.0597

Gnomad4 FIN exome

AF:

0.0582

Gnomad4 NFE exome

AF:

0.0628

Gnomad4 OTH exome

AF:

0.0580

GnomAD4 genome

AF:

0.0447

AC:

6797

AN:

152224

Hom.:

200

Cov.:

AF XY:

0.0440

AC XY:

3271

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0105

Gnomad4 AMR

AF:

0.0522

Gnomad4 ASJ

AF:

0.0806

Gnomad4 EAS

AF:

0.0129

Gnomad4 SAS

AF:

0.0509

Gnomad4 FIN

AF:

0.0500

Gnomad4 NFE

AF:

0.0627

Gnomad4 OTH

AF:

0.0508

Alfa

AF:

0.0222

Hom.:

Bravo

AF:

0.0434

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.45

DANN

Benign

0.84

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over