Variant rs1841043 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 0.646 in 151,762 control chromosomes in the GnomAD database, including 32,826 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 0.65 ( 32826 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.137

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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 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:

0.646

AC:

98035

AN:

151644

Hom.:

32809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.766

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.672

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.735

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.662

Gnomad NFE

AF:

0.760

Gnomad OTH

AF:

0.635

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

GnomAD4 genome

AF:

0.646

AC:

98100

AN:

151762

Hom.:

32826

Cov.:

AF XY:

0.641

AC XY:

47482

AN XY:

74128

show subpopulations

Gnomad4 AFR

AF:

0.477

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.672

Gnomad4 EAS

AF:

0.546

Gnomad4 SAS

AF:

0.735

Gnomad4 FIN

AF:

0.652

Gnomad4 NFE

AF:

0.760

Gnomad4 OTH

AF:

0.636

Alfa

AF:

0.729

Hom.:

49076

Bravo

AF:

0.630

Asia WGS

AF:

0.647

AC:

2251

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

DANN

Benign

0.54

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