Variant rs7955516 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 0.357 in 145,616 control chromosomes in the GnomAD database, including 9,261 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 0.36 ( 9261 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.36

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=-1.08).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 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:

0.357

AC:

51988

AN:

145494

Hom.:

9253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.406

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.451

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.389

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

GnomAD4 genome

AF:

0.357

AC:

52024

AN:

145616

Hom.:

9261

Cov.:

AF XY:

0.352

AC XY:

25055

AN XY:

71198

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.420

Gnomad4 ASJ

AF:

0.406

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.393

Gnomad4 OTH

AF:

0.383

Alfa

AF:

0.356

Hom.:

8125

Bravo

AF:

0.351

Asia WGS

AF:

0.224

AC:

780

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.016

DANN

Benign

0.21

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