Variant rs3129871 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 0.593 in 152,088 control chromosomes in the GnomAD database, including 27,309 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 0.59 ( 27309 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.37

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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:

0.593

AC:

90106

AN:

151970

Hom.:

27303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.677

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.662

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.655

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.647

Gnomad OTH

AF:

0.603

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

GnomAD4 genome

AF:

0.593

AC:

90140

AN:

152088

Hom.:

27309

Cov.:

AF XY:

0.596

AC XY:

44332

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.449

Gnomad4 AMR

AF:

0.633

Gnomad4 ASJ

AF:

0.662

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.657

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.647

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.653

Hom.:

52891

Bravo

AF:

0.585

Asia WGS

AF:

0.649

AC:

2261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.094

DANN

Benign

0.19

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