Variant rs255592 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 0.732 in 152,018 control chromosomes in the GnomAD database, including 40,961 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 0.73 ( 40961 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.960

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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.8 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:

0.732

AC:

111217

AN:

151900

Hom.:

40924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.774

Gnomad AMI

AF:

0.787

Gnomad AMR

AF:

0.811

Gnomad ASJ

AF:

0.762

Gnomad EAS

AF:

0.539

Gnomad SAS

AF:

0.616

Gnomad FIN

AF:

0.730

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.748

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

GnomAD4 genome

AF:

0.732

AC:

111309

AN:

152018

Hom.:

40961

Cov.:

AF XY:

0.734

AC XY:

54507

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.774

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.762

Gnomad4 EAS

AF:

0.539

Gnomad4 SAS

AF:

0.616

Gnomad4 FIN

AF:

0.730

Gnomad4 NFE

AF:

0.709

Gnomad4 OTH

AF:

0.750

Alfa

AF:

0.716

Hom.:

78144

Bravo

AF:

0.746

Asia WGS

AF:

0.642

AC:

2231

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.65

DANN

Benign

0.52

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