Variant 2-79651796-T-A 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_001282597.3(CTNNA2):c.102+138T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 701,446 control chromosomes in the GnomAD database, including 6,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.087 ( 1017 hom., cov: 32)

Exomes 𝑓: 0.12 ( 5242 hom. )

Consequence

CTNNA2
NM_001282597.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.459

Variant links:

Genes affected

CTNNA2 (HGNC:2510): (catenin alpha 2) Enables actin filament binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation; regulation of neuron migration; and regulation of neuron projection development. Located in cytoplasm. Implicated in complex cortical dysplasia with other brain malformations. [provided by Alliance of Genome Resources, Apr 2022]

CTNNA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

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

BP6

Variant 2-79651796-T-A is Benign according to our data. Variant chr2-79651796-T-A is described in ClinVar as [Benign]. Clinvar id is 1226238.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA2	NM_001282597.3 link	c.102+138T>A		intron_variant		ENST00000402739.9	NP_001269526.1	P26232-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNA2	ENST00000402739.9 link	c.102+138T>A		intron_variant		1	NM_001282597.3	ENSP00000384638.4		P26232-1

Frequencies

GnomAD3 genomes

AF:

0.0870

AC:

13244

AN:

152148

Hom.:

1011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0229

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0583

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.0783

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0974

Gnomad OTH

AF:

0.0860

GnomAD4 exome

AF:

0.119

AC:

65109

AN:

549180

Hom.:

5242

AF XY:

0.124

AC XY:

35663

AN XY:

286956

show subpopulations

Gnomad4 AFR exome

AF:

0.0223

Gnomad4 AMR exome

AF:

0.0441

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.303

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.0790

Gnomad4 NFE exome

AF:

0.0966

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.0870

AC:

13248

AN:

152266

Hom.:

1017

Cov.:

AF XY:

0.0882

AC XY:

6568

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0228

Gnomad4 AMR

AF:

0.0582

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.352

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.0783

Gnomad4 NFE

AF:

0.0973

Gnomad4 OTH

AF:

0.0885

Alfa

AF:

0.0889

Hom.:

Bravo

AF:

0.0830

Asia WGS

AF:

0.234

AC:

814

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

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.0

DANN

Benign

0.64

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