Variant rs6685280 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 0.747 in 152,140 control chromosomes in the GnomAD database, including 43,018 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 0.75 ( 43018 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

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 = 0.927 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:

0.747

AC:

113617

AN:

152022

Hom.:

43010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.812

Gnomad AMR

AF:

0.802

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.949

Gnomad SAS

AF:

0.741

Gnomad FIN

AF:

0.831

Gnomad MID

AF:

0.752

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.744

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

GnomAD4 genome

AF:

0.747

AC:

113650

AN:

152140

Hom.:

43018

Cov.:

AF XY:

0.753

AC XY:

55979

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.622

Gnomad4 AMR

AF:

0.802

Gnomad4 ASJ

AF:

0.741

Gnomad4 EAS

AF:

0.950

Gnomad4 SAS

AF:

0.740

Gnomad4 FIN

AF:

0.831

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.742

Alfa

AF:

0.769

Hom.:

71628

Bravo

AF:

0.741

Asia WGS

AF:

0.793

AC:

2757

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

0.22

DANN

Benign

0.19

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