Variant rs6506640 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 0.82 in 152,100 control chromosomes in the GnomAD database, including 51,221 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 0.82 ( 51221 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

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=-1.04).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 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:

0.820

AC:

124586

AN:

151982

Hom.:

51177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.808

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.776

Gnomad ASJ

AF:

0.912

Gnomad EAS

AF:

0.738

Gnomad SAS

AF:

0.864

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.927

Gnomad NFE

AF:

0.840

Gnomad OTH

AF:

0.841

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

GnomAD4 genome

AF:

0.820

AC:

124682

AN:

152100

Hom.:

51221

Cov.:

AF XY:

0.817

AC XY:

60707

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.808

Gnomad4 AMR

AF:

0.776

Gnomad4 ASJ

AF:

0.912

Gnomad4 EAS

AF:

0.738

Gnomad4 SAS

AF:

0.865

Gnomad4 FIN

AF:

0.778

Gnomad4 NFE

AF:

0.840

Gnomad4 OTH

AF:

0.836

Alfa

AF:

0.785

Hom.:

2371

Bravo

AF:

0.818

Asia WGS

AF:

0.755

AC:

2625

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.4

DANN

Benign

0.73

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