Variant rs7586540 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 0.893 in 152,120 control chromosomes in the GnomAD database, including 60,849 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 0.89 ( 60849 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.893

AC:

135694

AN:

152002

Hom.:

60787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.943

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.898

Gnomad ASJ

AF:

0.840

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.947

Gnomad FIN

AF:

0.899

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.852

Gnomad OTH

AF:

0.870

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

GnomAD4 genome

AF:

0.893

AC:

135816

AN:

152120

Hom.:

60849

Cov.:

AF XY:

0.897

AC XY:

66679

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.943

Gnomad4 AMR

AF:

0.899

Gnomad4 ASJ

AF:

0.840

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.946

Gnomad4 FIN

AF:

0.899

Gnomad4 NFE

AF:

0.852

Gnomad4 OTH

AF:

0.872

Alfa

AF:

0.867

Hom.:

36160

Bravo

AF:

0.894

Asia WGS

AF:

0.975

AC:

3389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.43

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