Variant rs7894582 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 0.0652 in 152,182 control chromosomes in the GnomAD database, including 427 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 0.065 ( 427 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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:

0.0652

AC:

9907

AN:

152064

Hom.:

423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0356

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0270

Gnomad FIN

AF:

0.0839

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0457

Gnomad OTH

AF:

0.0512

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

GnomAD4 genome

AF:

0.0652

AC:

9929

AN:

152182

Hom.:

427

Cov.:

AF XY:

0.0651

AC XY:

4844

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.120

Gnomad4 AMR

AF:

0.0355

Gnomad4 ASJ

AF:

0.0360

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0270

Gnomad4 FIN

AF:

0.0839

Gnomad4 NFE

AF:

0.0457

Gnomad4 OTH

AF:

0.0521

Alfa

AF:

0.0451

Hom.:

254

Bravo

AF:

0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.77

DANN

Benign

0.51

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