Variant rs1917858 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 0.533 in 151,912 control chromosomes in the GnomAD database, including 25,065 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 0.53 ( 25065 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0380

Variant links:

Genome browser will be placed here

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 (SAS) allele frequency at 95% confidence interval = 0.709 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:

0.533

AC:

80943

AN:

151794

Hom.:

25049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.674

Gnomad ASJ

AF:

0.604

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.727

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.530

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

GnomAD4 genome

AF:

0.533

AC:

80976

AN:

151912

Hom.:

25065

Cov.:

AF XY:

0.538

AC XY:

39931

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.674

Gnomad4 ASJ

AF:

0.604

Gnomad4 EAS

AF:

0.333

Gnomad4 SAS

AF:

0.729

Gnomad4 FIN

AF:

0.655

Gnomad4 NFE

AF:

0.677

Gnomad4 OTH

AF:

0.535

Alfa

AF:

0.587

Hom.:

3509

Bravo

AF:

0.516

Asia WGS

AF:

0.538

AC:

1868

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.0

DANN

Benign

0.67

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