Variant rs6436346 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 0.707 in 152,034 control chromosomes in the GnomAD database, including 38,493 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 0.71 ( 38493 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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:

0.707

AC:

107359

AN:

151916

Hom.:

38442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.819

Gnomad AMI

AF:

0.733

Gnomad AMR

AF:

0.621

Gnomad ASJ

AF:

0.680

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.629

Gnomad MID

AF:

0.764

Gnomad NFE

AF:

0.681

Gnomad OTH

AF:

0.694

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

GnomAD4 genome

AF:

0.707

AC:

107461

AN:

152034

Hom.:

38493

Cov.:

AF XY:

0.702

AC XY:

52151

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.820

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.680

Gnomad4 EAS

AF:

0.600

Gnomad4 SAS

AF:

0.677

Gnomad4 FIN

AF:

0.629

Gnomad4 NFE

AF:

0.681

Gnomad4 OTH

AF:

0.693

Alfa

AF:

0.685

Hom.:

72405

Bravo

AF:

0.710

Asia WGS

AF:

0.609

AC:

2120

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

DANN

Benign

0.34

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