Variant rs8138979 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1

The ENST00000458318.2(ENSG00000224277):n.308-1G>A variant causes a splice acceptor, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,242 control chromosomes in the GnomAD database, including 19,108 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 ( 19107 hom., cov: 30)

Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

ENST00000458318.2 splice_acceptor, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.973

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105372957	XR_938078.2 linkuse as main transcript	n.1129-1G>A	splice_acceptor_variant, non_coding_transcript_variant
LOC105372957	XR_938075.2 linkuse as main transcript	n.1129-1G>A	splice_acceptor_variant, non_coding_transcript_variant
LOC105372957	XR_938076.1 linkuse as main transcript	n.610-1G>A	splice_acceptor_variant, non_coding_transcript_variant
LOC105372957	XR_938077.2 linkuse as main transcript	n.1129-1G>A	splice_acceptor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000458318.2 linkuse as main transcript	n.308-1G>A		splice_acceptor_variant, non_coding_transcript_variant		3
	ENST00000454863.4 linkuse as main transcript	n.308-1G>A		splice_acceptor_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.419

AC:

63318

AN:

151108

Hom.:

19049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.846

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.308

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.222

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.420

AC:

63442

AN:

151216

Hom.:

19107

Cov.:

AF XY:

0.419

AC XY:

30917

AN XY:

73794

show subpopulations

Gnomad4 AFR

AF:

0.846

Gnomad4 AMR

AF:

0.405

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.448

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.390

Alfa

AF:

0.336

Hom.:

3936

Bravo

AF:

0.453

Asia WGS

AF:

0.483

AC:

1675

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.9

DANN

Benign

0.56

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over