Variant rs7282671 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 0.192 in 152,270 control chromosomes in the GnomAD database, including 2,996 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 0.19 ( 2996 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.961

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 (AMR) allele frequency at 95% confidence interval = 0.25 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:

0.192

AC:

29182

AN:

152152

Hom.:

2992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.0363

Gnomad SAS

AF:

0.0687

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.200

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

GnomAD4 genome

AF:

0.192

AC:

29195

AN:

152270

Hom.:

2996

Cov.:

AF XY:

0.188

AC XY:

14017

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.0360

Gnomad4 SAS

AF:

0.0681

Gnomad4 FIN

AF:

0.136

Gnomad4 NFE

AF:

0.185

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.145

Hom.:

399

Bravo

AF:

0.204

Asia WGS

AF:

0.0790

AC:

275

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.9

DANN

Benign

0.64

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