2-80437314-T-G

Position:

• chr2-80437314-T-G

Variant summary

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

The NM_001282597.3(CTNNA2):​c.1290+17713T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,154 control chromosomes in the GnomAD database, including 20,814 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 0.44 (20814 hom., cov: 33)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNA2	NM_001282597.3	c.1290+17713T>G		intron_variant		ENST00000402739.9	NP_001269526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNA2	ENST00000402739.9	c.1290+17713T>G		intron_variant		1	NM_001282597.3	ENSP00000384638.4

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66474 AN: 152036 Hom.: 20756 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.438 AC: 66596 AN: 152154 Hom.: 20814 Cov.: 33 AF XY: 0.441 AC XY: 32794 AN XY: 74398

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.384

Alfa AF: 0.251 Hom.: 10644

Bravo AF: 0.475

Asia WGS AF: 0.591 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.38

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: rs10195705; hg19: chr2-80664439;