Variant 19-48638275-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001217.5(CA11):c.962-131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,174,836 control chromosomes in the GnomAD database, including 422,040 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 0.82 ( 50887 hom., cov: 24)

Exomes 𝑓: 0.85 ( 371153 hom. )

Consequence

CA11
NM_001217.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740

Variant links:

Genes affected

CA11 (HGNC:1370): (carbonic anhydrase 11) 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. They show extensive diversity in tissue distribution and in their subcellular localization. CA XI is likely a secreted protein, however, radical changes at active site residues completely conserved in CA isozymes with catalytic activity, make it unlikely that it has carbonic anhydrase activity. It shares properties in common with two other acatalytic CA isoforms, CA VIII and CA X. CA XI is most abundantly expressed in brain, and may play a general role in the central nervous system. [provided by RefSeq, Jul 2008]

CA11 links:

SEC1P (HGNC:44149): (secretory blood group 1, pseudogene) Predicted to enable galactoside 2-alpha-L-fucosyltransferase activity. Predicted to act upstream of or within protein glycosylation. [provided by Alliance of Genome Resources, Apr 2022]

SEC1P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
CA11	NM_001217.5 link	c.962-131A>G	intron_variant		ENST00000084798.9	NP_001208.2	O75493
CA11	NR_136241.2 link	n.2129A>G	non_coding_transcript_exon_variant	8/9
SEC1P	NR_004401.2 link	n.108+129T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CA11	ENST00000084798.9 link	c.962-131A>G		intron_variant		1	NM_001217.5	ENSP00000084798.3		O75493

Frequencies

GnomAD3 genomes

AF:

0.822

AC:

123303

AN:

149982

Hom.:

50854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.817

Gnomad AMR

AF:

0.827

Gnomad ASJ

AF:

0.855

Gnomad EAS

AF:

0.629

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.821

Gnomad MID

AF:

0.885

Gnomad NFE

AF:

0.853

Gnomad OTH

AF:

0.839

GnomAD3 exomes

AF:

0.830

AC:

11322

AN:

13648

Hom.:

4700

AF XY:

0.833

AC XY:

5621

AN XY:

6748

show subpopulations

Gnomad AFR exome

AF:

0.788

Gnomad AMR exome

AF:

0.827

Gnomad ASJ exome

AF:

0.814

Gnomad EAS exome

AF:

0.680

Gnomad SAS exome

AF:

0.755

Gnomad FIN exome

AF:

0.812

Gnomad NFE exome

AF:

0.861

Gnomad OTH exome

AF:

0.872

GnomAD4 exome

AF:

0.849

AC:

870220

AN:

1024736

Hom.:

371153

Cov.:

AF XY:

0.850

AC XY:

411943

AN XY:

484868

show subpopulations

Gnomad4 AFR exome

AF:

0.782

Gnomad4 AMR exome

AF:

0.817

Gnomad4 ASJ exome

AF:

0.841

Gnomad4 EAS exome

AF:

0.541

Gnomad4 SAS exome

AF:

0.808

Gnomad4 FIN exome

AF:

0.806

Gnomad4 NFE exome

AF:

0.862

Gnomad4 OTH exome

AF:

0.845

GnomAD4 genome

AF:

0.822

AC:

123396

AN:

150100

Hom.:

50887

Cov.:

AF XY:

0.819

AC XY:

59939

AN XY:

73218

show subpopulations

Gnomad4 AFR

AF:

0.792

Gnomad4 AMR

AF:

0.827

Gnomad4 ASJ

AF:

0.855

Gnomad4 EAS

AF:

0.629

Gnomad4 SAS

AF:

0.794

Gnomad4 FIN

AF:

0.821

Gnomad4 NFE

AF:

0.853

Gnomad4 OTH

AF:

0.840

Alfa

AF:

0.822

Hom.:

7117

Bravo

AF:

0.823

Asia WGS

AF:

0.707

AC:

2455

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.2

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over