Variant chr2-79870079-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001282597.3(CTNNA2):c.585+144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 1,055,522 control chromosomes in the GnomAD database, including 1,621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 505 hom., cov: 33)

Exomes 𝑓: 0.023 ( 1116 hom. )

Consequence

CTNNA2
NM_001282597.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0840

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-79870079-C-T is Benign according to our data. Variant chr2-79870079-C-T is described in ClinVar as [Benign]. Clinvar id is 1238448.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA2	NM_001282597.3 link	c.585+144C>T		intron_variant		ENST00000402739.9	NP_001269526.1	P26232-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CTNNA2	ENST00000402739.9 link	c.585+144C>T	intron_variant	1	NM_001282597.3	ENSP00000384638.4	P26232-1
CTNNA2	ENST00000496558.5 link	c.585+144C>T	intron_variant	1		ENSP00000419295.1	P26232-2
CTNNA2	ENST00000466387.5 link	c.585+144C>T	intron_variant	2		ENSP00000418191.1	P26232-2
CTNNA2	ENST00000629316.2 link	c.585+144C>T	intron_variant	2		ENSP00000486160.1	P26232-3

Frequencies

GnomAD3 genomes

AF:

0.0559

AC:

8503

AN:

152084

Hom.:

503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0310

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.0298

Gnomad FIN

AF:

0.0321

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.00960

Gnomad OTH

AF:

0.0468

GnomAD4 exome

AF:

0.0228

AC:

20575

AN:

903320

Hom.:

1116

AF XY:

0.0222

AC XY:

10190

AN XY:

458630

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.0251

Gnomad4 ASJ exome

AF:

0.0272

Gnomad4 EAS exome

AF:

0.206

Gnomad4 SAS exome

AF:

0.0284

Gnomad4 FIN exome

AF:

0.0244

Gnomad4 NFE exome

AF:

0.00835

Gnomad4 OTH exome

AF:

0.0302

GnomAD4 genome

AF:

0.0559

AC:

8515

AN:

152202

Hom.:

505

Cov.:

AF XY:

0.0577

AC XY:

4295

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.0309

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.182

Gnomad4 SAS

AF:

0.0301

Gnomad4 FIN

AF:

0.0321

Gnomad4 NFE

AF:

0.00957

Gnomad4 OTH

AF:

0.0501

Alfa

AF:

0.0358

Hom.:

Bravo

AF:

0.0605

Asia WGS

AF:

0.133

AC:

461

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.7

DANN

Benign

0.71

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