2-79822592-C-T

Position:

• chr2-79822592-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001282597.3(CTNNA2):​c.299-35421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,836 control chromosomes in the GnomAD database, including 17,578 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 0.47 (17578 hom., cov: 30)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA2	NM_001282597.3	c.299-35421C>T		intron_variant		ENST00000402739.9	NP_001269526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNA2	ENST00000402739.9	c.299-35421C>T		intron_variant		1	NM_001282597.3	ENSP00000384638.4

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71223 AN: 151716 Hom.: 17559 Cov.: 30

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.469 AC: 71272 AN: 151836 Hom.: 17578 Cov.: 30 AF XY: 0.469 AC XY: 34802 AN XY: 74216

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.500

Alfa AF: 0.519 Hom.: 12377

Bravo AF: 0.466

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0090
DANN	Benign	0.47

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: rs4852531; hg19: chr2-80049718;