5-138753397-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_134244.1(CTNNA1-AS1):n.402+126C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.60 (21305 hom., cov: 16)
  • Exomes 𝑓: 0.71 (51106 hom.)
• Consequence: CTNNA1-AS1 NR_134244.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.534

Genes affected

CTNNA1-AS1 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 5-138753397-G-A is Benign according to our data. Variant chr5-138753397-G-A is described in ClinVar as [Benign]. Clinvar id is 1292329.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA1-AS1	NR_134244.1	n.402+126C>T		intron_variant, non_coding_transcript_variant
CTNNA1	NM_001903.5			upstream_gene_variant		ENST00000302763.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTNNA1	ENST00000302763.12			upstream_gene_variant		1	NM_001903.5	P1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 70089 AN: 117018 Hom.: 21299 Cov.: 16

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.715 AC: 140052 AN: 195930 Hom.: 51106 Cov.: 0 AF XY: 0.713 AC XY: 71459 AN XY: 100278

Gnomad4 AFR exome AF: 0.499

Gnomad4 AMR exome AF: 0.742

Gnomad4 ASJ exome AF: 0.672

Gnomad4 EAS exome AF: 0.930

Gnomad4 SAS exome AF: 0.701

Gnomad4 FIN exome AF: 0.690

Gnomad4 NFE exome AF: 0.698

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.599 AC: 70112 AN: 117084 Hom.: 21305 Cov.: 16 AF XY: 0.605 AC XY: 34302 AN XY: 56710

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.647

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	17
Dann	Benign	0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs62384262; hg19: chr5-138089086; COSMIC: COSV57071175;