Variant rs1501572 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 0.398 in 151,948 control chromosomes in the GnomAD database, including 12,139 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 0.40 ( 12139 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.191

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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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:

0.397

AC:

60303

AN:

151830

Hom.:

12093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.389

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

GnomAD4 genome

AF:

0.398

AC:

60401

AN:

151948

Hom.:

12139

Cov.:

AF XY:

0.400

AC XY:

29739

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.446

Gnomad4 AMR

AF:

0.341

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.431

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.395

Alfa

AF:

0.375

Hom.:

1312

Bravo

AF:

0.394

Asia WGS

AF:

0.477

AC:

1659

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

DANN

Benign

0.77

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