rs11883960

chr2-80049969-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+140172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,120 control chromosomes in the GnomAD database, including 1,555 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 0.11 (1555 hom., cov: 32)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA2	NM_001282597.3	c.1056+140172C>T		intron_variant		ENST00000402739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA2	ENST00000402739.9	c.1056+140172C>T		intron_variant		1	NM_001282597.3
CTNNA2	ENST00000496558.5	c.1056+140172C>T		intron_variant		1		P1
CTNNA2	ENST00000466387.5	c.1056+140172C>T		intron_variant		2		P1
CTNNA2	ENST00000629316.2	c.1056+140172C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15998 AN: 152002 Hom.: 1547 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.106 AC: 16058 AN: 152120 Hom.: 1555 Cov.: 32 AF XY: 0.104 AC XY: 7751 AN XY: 74386

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0297

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0432

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0654 Hom.: 297

Bravo AF: 0.117

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.97
Dann	Benign	0.53

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: rs11883960; hg19: chr2-80277095;