Variant rs6950683 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 0.865 in 151,502 control chromosomes in the GnomAD database, including 57,006 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 0.86 ( 57006 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 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:

0.865

AC:

130916

AN:

151394

Hom.:

56951

Cov.:

show subpopulations

Gnomad AFR

AF:

0.963

Gnomad AMI

AF:

0.799

Gnomad AMR

AF:

0.889

Gnomad ASJ

AF:

0.861

Gnomad EAS

AF:

0.764

Gnomad SAS

AF:

0.805

Gnomad FIN

AF:

0.735

Gnomad MID

AF:

0.913

Gnomad NFE

AF:

0.832

Gnomad OTH

AF:

0.873

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

GnomAD4 genome

AF:

0.865

AC:

131026

AN:

151502

Hom.:

57006

Cov.:

AF XY:

0.861

AC XY:

63732

AN XY:

74024

show subpopulations

Gnomad4 AFR

AF:

0.963

Gnomad4 AMR

AF:

0.889

Gnomad4 ASJ

AF:

0.861

Gnomad4 EAS

AF:

0.764

Gnomad4 SAS

AF:

0.804

Gnomad4 FIN

AF:

0.735

Gnomad4 NFE

AF:

0.832

Gnomad4 OTH

AF:

0.874

Alfa

AF:

0.833

Hom.:

6180

Bravo

AF:

0.879

Asia WGS

AF:

0.793

AC:

2712

AN:

3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.1

DANN

Benign

0.24

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