Variant rs7047687 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 0.624 in 151,876 control chromosomes in the GnomAD database, including 29,771 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 0.62 ( 29771 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.404

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 (EAS) allele frequency at 95% confidence interval = 0.853 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:

0.624

AC:

94648

AN:

151758

Hom.:

29731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.874

Gnomad SAS

AF:

0.714

Gnomad FIN

AF:

0.591

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.629

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

GnomAD4 genome

AF:

0.624

AC:

94744

AN:

151876

Hom.:

29771

Cov.:

AF XY:

0.628

AC XY:

46570

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.646

Gnomad4 ASJ

AF:

0.607

Gnomad4 EAS

AF:

0.874

Gnomad4 SAS

AF:

0.714

Gnomad4 FIN

AF:

0.591

Gnomad4 NFE

AF:

0.602

Gnomad4 OTH

AF:

0.634

Alfa

AF:

0.473

Hom.:

1247

Bravo

AF:

0.628

Asia WGS

AF:

0.790

AC:

2739

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.83

DANN

Benign

0.26

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