2-79523465-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001282597.3(CTNNA2):c.-6+10258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,994 control chromosomes in the GnomAD database, including 32,906 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.66 (32906 hom., cov: 33)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.29

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 2-79523465-G-T is Benign according to our data. Variant chr2-79523465-G-T is described in ClinVar as [Benign]. Clinvar id is 1249105.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA2	NM_001282597.3	c.-6+10258G>T		intron_variant		ENST00000402739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA2	ENST00000402739.9	c.-6+10258G>T		intron_variant		1	NM_001282597.3

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99812 AN: 151878 Hom.: 32878 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.657 AC: 99887 AN: 151994 Hom.: 32906 Cov.: 33 AF XY: 0.655 AC XY: 48673 AN XY: 74294

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.647

Alfa AF: 0.669 Hom.: 22016

Bravo AF: 0.647

Asia WGS AF: 0.654 AC: 2278 AN: 3478

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

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.3
Dann	Benign	0.19

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: rs10206130; hg19: chr2-79750591;