Variant rs6556398 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 0.764 in 152,056 control chromosomes in the GnomAD database, including 45,234 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 0.76 ( 45234 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.763

AC:

115998

AN:

151938

Hom.:

45181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.932

Gnomad AMI

AF:

0.768

Gnomad AMR

AF:

0.751

Gnomad ASJ

AF:

0.725

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.796

Gnomad NFE

AF:

0.692

Gnomad OTH

AF:

0.777

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

GnomAD4 genome

AF:

0.764

AC:

116110

AN:

152056

Hom.:

45234

Cov.:

AF XY:

0.762

AC XY:

56653

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.932

Gnomad4 AMR

AF:

0.751

Gnomad4 ASJ

AF:

0.725

Gnomad4 EAS

AF:

0.569

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.675

Gnomad4 NFE

AF:

0.692

Gnomad4 OTH

AF:

0.775

Alfa

AF:

0.739

Hom.:

5216

Bravo

AF:

0.770

Asia WGS

AF:

0.720

AC:

2504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.31

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