Variant rs7739700 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 0.339 in 151,988 control chromosomes in the GnomAD database, including 9,212 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 0.34 ( 9212 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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:

0.339

AC:

51499

AN:

151872

Hom.:

9208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.325

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

GnomAD4 genome

AF:

0.339

AC:

51533

AN:

151988

Hom.:

9212

Cov.:

AF XY:

0.341

AC XY:

25343

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.314

Gnomad4 ASJ

AF:

0.332

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.387

Gnomad4 OTH

AF:

0.329

Alfa

AF:

0.272

Hom.:

1121

Bravo

AF:

0.328

Asia WGS

AF:

0.401

AC:

1391

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.84

DANN

Benign

0.74

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