Variant rs3923037 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 0.419 in 152,102 control chromosomes in the GnomAD database, including 14,131 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 0.42 ( 14131 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165

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 (EAS) allele frequency at 95% confidence interval = 0.828 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:

0.419

AC:

63664

AN:

151984

Hom.:

14125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.849

Gnomad SAS

AF:

0.598

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.419

AC:

63702

AN:

152102

Hom.:

14131

Cov.:

AF XY:

0.423

AC XY:

31480

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.849

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.370

Gnomad4 NFE

AF:

0.360

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.357

Hom.:

4294

Bravo

AF:

0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.9

DANN

Benign

0.65

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