rs6547313

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001282597.3(CTNNA2):​c.1291-59911A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,876 control chromosomes in the GnomAD database, including 14,790 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 0.42 ( 14790 hom., cov: 32)

Consequence

CTNNA2
NM_001282597.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.163
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTNNA2NM_001282597.3 linkuse as main transcriptc.1291-59911A>G intron_variant ENST00000402739.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTNNA2ENST00000402739.9 linkuse as main transcriptc.1291-59911A>G intron_variant 1 NM_001282597.3 P26232-1

Frequencies

GnomAD3 genomes
AF:
0.415
AC:
63027
AN:
151760
Hom.:
14765
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.351
Gnomad AMR
AF:
0.474
Gnomad ASJ
AF:
0.374
Gnomad EAS
AF:
0.681
Gnomad SAS
AF:
0.513
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.300
Gnomad OTH
AF:
0.405
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.415
AC:
63098
AN:
151876
Hom.:
14790
Cov.:
32
AF XY:
0.416
AC XY:
30906
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.475
Gnomad4 ASJ
AF:
0.374
Gnomad4 EAS
AF:
0.682
Gnomad4 SAS
AF:
0.511
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.300
Gnomad4 OTH
AF:
0.409
Alfa
AF:
0.344
Hom.:
2040
Bravo
AF:
0.447
Asia WGS
AF:
0.586
AC:
2034
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
0.66
DANN
Benign
0.55

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6547313; hg19: chr2-80712196; API