Variant rs6578974 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 0.167 in 151,996 control chromosomes in the GnomAD database, including 3,950 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 0.17 ( 3950 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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:

0.167

AC:

25368

AN:

151878

Hom.:

3937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0813

Gnomad ASJ

AF:

0.0949

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0421

Gnomad FIN

AF:

0.0730

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0792

Gnomad OTH

AF:

0.138

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

GnomAD4 genome

AF:

0.167

AC:

25412

AN:

151996

Hom.:

3950

Cov.:

AF XY:

0.161

AC XY:

11952

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.415

Gnomad4 AMR

AF:

0.0811

Gnomad4 ASJ

AF:

0.0949

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.0418

Gnomad4 FIN

AF:

0.0730

Gnomad4 NFE

AF:

0.0792

Gnomad4 OTH

AF:

0.137

Alfa

AF:

0.0805

Hom.:

1009

Bravo

AF:

0.181

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.083

DANN

Benign

0.65

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