rs2974142

Positions:

• chr2-79935069-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.1056+25272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,106 control chromosomes in the GnomAD database, including 41,638 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 0.73 (41638 hom., cov: 32)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA2	NM_001282597.3	c.1056+25272C>T		intron_variant		ENST00000402739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA2	ENST00000402739.9	c.1056+25272C>T		intron_variant		1	NM_001282597.3
CTNNA2	ENST00000496558.5	c.1056+25272C>T		intron_variant		1		P1
CTNNA2	ENST00000466387.5	c.1056+25272C>T		intron_variant		2		P1
CTNNA2	ENST00000629316.2	c.1056+25272C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111226 AN: 151988 Hom.: 41585 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.732 AC: 111337 AN: 152106 Hom.: 41638 Cov.: 32 AF XY: 0.731 AC XY: 54335 AN XY: 74356

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.696

Alfa AF: 0.674 Hom.: 20614

Bravo AF: 0.749

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.50

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: rs2974142; hg19: chr2-80162195;