Variant rs6467410 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.868 in 152,218 control chromosomes in the GnomAD database, including 57,637 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 0.87 ( 57637 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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:

0.868

AC:

132074

AN:

152100

Hom.:

57573

Cov.:

show subpopulations

Gnomad AFR

AF:

0.921

Gnomad AMI

AF:

0.750

Gnomad AMR

AF:

0.881

Gnomad ASJ

AF:

0.795

Gnomad EAS

AF:

0.984

Gnomad SAS

AF:

0.908

Gnomad FIN

AF:

0.848

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.851

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

GnomAD4 genome

AF:

0.868

AC:

132201

AN:

152218

Hom.:

57637

Cov.:

AF XY:

0.870

AC XY:

64710

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.922

Gnomad4 AMR

AF:

0.882

Gnomad4 ASJ

AF:

0.795

Gnomad4 EAS

AF:

0.984

Gnomad4 SAS

AF:

0.908

Gnomad4 FIN

AF:

0.848

Gnomad4 NFE

AF:

0.831

Gnomad4 OTH

AF:

0.854

Alfa

AF:

0.854

Hom.:

6904

Bravo

AF:

0.873

Asia WGS

AF:

0.939

AC:

3263

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.72

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