Variant rs702139 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 0.667 in 151,942 control chromosomes in the GnomAD database, including 34,266 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 0.67 ( 34266 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.946

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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:

0.667

AC:

101285

AN:

151824

Hom.:

34230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.728

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.801

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.743

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.639

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

GnomAD4 genome

AF:

0.667

AC:

101365

AN:

151942

Hom.:

34266

Cov.:

AF XY:

0.671

AC XY:

49827

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.722

Gnomad4 AMR

AF:

0.687

Gnomad4 ASJ

AF:

0.531

Gnomad4 EAS

AF:

0.802

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.743

Gnomad4 NFE

AF:

0.627

Gnomad4 OTH

AF:

0.641

Alfa

AF:

0.620

Hom.:

7032

Bravo

AF:

0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.7

DANN

Benign

0.70

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