5-138753397-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000522227.5(CTNNA1):​c.-2-28526G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000026 ( 0 hom., cov: 16)
Exomes 𝑓: 0.000046 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CTNNA1
ENST00000522227.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.534
Variant links:
Genes affected
CTNNA1 (HGNC:2509): (catenin alpha 1) This gene encodes a member of the catenin family of proteins that play an important role in cell adhesion process by connecting cadherins located on the plasma membrane to the actin filaments inside the cell. The encoded mechanosensing protein contains three vinculin homology domains and undergoes conformational changes in response to cytoskeletal tension, resulting in the reconfiguration of cadherin-actin filament connections. Certain mutations in this gene cause butterfly-shaped pigment dystrophy. [provided by RefSeq, May 2016]
CTNNA1-AS1 (HGNC:55535): (CTNNA1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BS2
High AC in GnomAdExome4 at 9 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CTNNA1NM_001903.5 linkc.-116G>C upstream_gene_variant ENST00000302763.12 NP_001894.2 P35221-1A0A384MDY0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTNNA1ENST00000302763.12 linkc.-116G>C upstream_gene_variant 1 NM_001903.5 ENSP00000304669.7 P35221-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
3
AN:
117348
Hom.:
0
Cov.:
16
FAILED QC
Gnomad AFR
AF:
0.0000309
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000809
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000187
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000459
AC:
9
AN:
196038
Hom.:
0
Cov.:
0
AF XY:
0.0000399
AC XY:
4
AN XY:
100326
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000535
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000560
Gnomad4 OTH exome
AF:
0.0000805
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000256
AC:
3
AN:
117414
Hom.:
0
Cov.:
16
AF XY:
0.0000352
AC XY:
2
AN XY:
56884
show subpopulations
Gnomad4 AFR
AF:
0.0000308
Gnomad4 AMR
AF:
0.0000809
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000187
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
16
DANN
Benign
0.63

Splicing

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: rs62384262; hg19: chr5-138089086; API