Variant rs1338657 details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.422 in 151,602 control chromosomes in the GnomAD database, including 13,831 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 ( 13831 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.422

AC:

63883

AN:

151482

Hom.:

13814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.421

Gnomad AMR

AF:

0.518

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.576

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.438

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

GnomAD4 genome

AF:

0.422

AC:

63938

AN:

151602

Hom.:

13831

Cov.:

AF XY:

0.426

AC XY:

31563

AN XY:

74046

show subpopulations

Gnomad4 AFR

AF:

0.347

Gnomad4 AMR

AF:

0.518

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.576

Gnomad4 SAS

AF:

0.490

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.423

Gnomad4 OTH

AF:

0.439

Alfa

AF:

0.431

Hom.:

16646

Bravo

AF:

0.425

Asia WGS

AF:

0.516

AC:

1790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.13

DANN

Benign

0.62

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