Variant rs1840054 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 0.435 in 151,906 control chromosomes in the GnomAD database, including 17,085 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 0.43 ( 17085 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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:

0.435

AC:

66029

AN:

151792

Hom.:

17091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.823

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.612

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.482

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

GnomAD4 genome

AF:

0.435

AC:

66030

AN:

151906

Hom.:

17085

Cov.:

AF XY:

0.440

AC XY:

32665

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.593

Gnomad4 EAS

AF:

0.823

Gnomad4 SAS

AF:

0.536

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.526

Hom.:

27759

Bravo

AF:

0.424

Asia WGS

AF:

0.633

AC:

2198

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.055

DANN

Benign

0.82

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