Variant rs6985069 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 0.672 in 152,022 control chromosomes in the GnomAD database, including 34,882 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 0.67 ( 34882 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167

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 (EAS) allele frequency at 95% confidence interval = 0.844 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:

0.672

AC:

102055

AN:

151904

Hom.:

34870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.608

Gnomad ASJ

AF:

0.800

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.770

Gnomad FIN

AF:

0.666

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.727

Gnomad OTH

AF:

0.683

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

GnomAD4 genome

AF:

0.672

AC:

102111

AN:

152022

Hom.:

34882

Cov.:

AF XY:

0.670

AC XY:

49772

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.608

Gnomad4 ASJ

AF:

0.800

Gnomad4 EAS

AF:

0.865

Gnomad4 SAS

AF:

0.770

Gnomad4 FIN

AF:

0.666

Gnomad4 NFE

AF:

0.727

Gnomad4 OTH

AF:

0.683

Alfa

AF:

0.674

Hom.:

5510

Bravo

AF:

0.663

Asia WGS

AF:

0.776

AC:

2698

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.6

DANN

Benign

0.75

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