Variant rs1932420 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,864 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 0.26 ( 5864 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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:

0.261

AC:

39629

AN:

151912

Hom.:

5879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.303

Gnomad OTH

AF:

0.311

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

GnomAD4 genome

AF:

0.261

AC:

39622

AN:

152030

Hom.:

5864

Cov.:

AF XY:

0.262

AC XY:

19493

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.447

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.303

Gnomad4 OTH

AF:

0.306

Alfa

AF:

0.290

Hom.:

3237

Bravo

AF:

0.260

Asia WGS

AF:

0.320

AC:

1114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.64

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