Variant rs255414 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 0.769 in 151,928 control chromosomes in the GnomAD database, including 45,534 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 0.77 ( 45534 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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:

0.769

AC:

116761

AN:

151810

Hom.:

45496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.813

Gnomad ASJ

AF:

0.797

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.850

Gnomad FIN

AF:

0.854

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.755

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

GnomAD4 genome

AF:

0.769

AC:

116858

AN:

151928

Hom.:

45534

Cov.:

AF XY:

0.776

AC XY:

57644

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.650

Gnomad4 AMR

AF:

0.813

Gnomad4 ASJ

AF:

0.797

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.851

Gnomad4 FIN

AF:

0.854

Gnomad4 NFE

AF:

0.795

Gnomad4 OTH

AF:

0.757

Alfa

AF:

0.799

Hom.:

59304

Bravo

AF:

0.760

Asia WGS

AF:

0.906

AC:

3118

AN:

3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.90

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