rs2078520

Positions:

• chr2-80165519-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.1057-227692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,034 control chromosomes in the GnomAD database, including 6,685 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 0.24 (6685 hom., cov: 32)
• Consequence: CTNNA2 NM_001282597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

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 (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA2	NM_001282597.3	c.1057-227692C>T		intron_variant		ENST00000402739.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA2	ENST00000402739.9	c.1057-227692C>T		intron_variant		1	NM_001282597.3
CTNNA2	ENST00000496558.5	c.1057-227692C>T		intron_variant		1		P1
CTNNA2	ENST00000466387.5	c.1057-227692C>T		intron_variant		2		P1
CTNNA2	ENST00000629316.2	c.1057-227692C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36714 AN: 151916 Hom.: 6655 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0851

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.242 AC: 36807 AN: 152034 Hom.: 6685 Cov.: 32 AF XY: 0.241 AC XY: 17903 AN XY: 74292

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.0851

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.0834

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.207

Alfa AF: 0.163 Hom.: 1378

Bravo AF: 0.257

Asia WGS AF: 0.282 AC: 978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.15

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: rs2078520; hg19: chr2-80392645;