Variant rs6753768 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 0.718 in 151,966 control chromosomes in the GnomAD database, including 39,682 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 0.72 ( 39682 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.371

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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:

0.718

AC:

109070

AN:

151848

Hom.:

39652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.759

Gnomad EAS

AF:

0.990

Gnomad SAS

AF:

0.812

Gnomad FIN

AF:

0.730

Gnomad MID

AF:

0.675

Gnomad NFE

AF:

0.740

Gnomad OTH

AF:

0.742

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

GnomAD4 genome

AF:

0.718

AC:

109155

AN:

151966

Hom.:

39682

Cov.:

AF XY:

0.722

AC XY:

53621

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.746

Gnomad4 ASJ

AF:

0.759

Gnomad4 EAS

AF:

0.990

Gnomad4 SAS

AF:

0.812

Gnomad4 FIN

AF:

0.730

Gnomad4 NFE

AF:

0.740

Gnomad4 OTH

AF:

0.744

Alfa

AF:

0.723

Hom.:

6325

Bravo

AF:

0.715

Asia WGS

AF:

0.873

AC:

3034

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.25

DANN

Benign

0.70

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