Variant rs1479137 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 0.385 in 152,046 control chromosomes in the GnomAD database, including 13,420 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 0.39 ( 13420 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.380

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 (NFE) allele frequency at 95% confidence interval = 0.505 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:

0.386

AC:

58577

AN:

151926

Hom.:

13419

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.634

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.610

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.385

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

GnomAD4 genome

AF:

0.385

AC:

58585

AN:

152046

Hom.:

13420

Cov.:

AF XY:

0.389

AC XY:

28864

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.341

Gnomad4 ASJ

AF:

0.536

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.610

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.322

Hom.:

988

Bravo

AF:

0.359

Asia WGS

AF:

0.278

AC:

966

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

DANN

Benign

0.43

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