Variant rs7787173 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 0.831 in 152,230 control chromosomes in the GnomAD database, including 52,927 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 0.83 ( 52927 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.564

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 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:

0.831

AC:

126409

AN:

152112

Hom.:

52890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.740

Gnomad AMI

AF:

0.965

Gnomad AMR

AF:

0.879

Gnomad ASJ

AF:

0.914

Gnomad EAS

AF:

0.908

Gnomad SAS

AF:

0.691

Gnomad FIN

AF:

0.908

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.862

Gnomad OTH

AF:

0.838

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

GnomAD4 genome

AF:

0.831

AC:

126498

AN:

152230

Hom.:

52927

Cov.:

AF XY:

0.831

AC XY:

61847

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.740

Gnomad4 AMR

AF:

0.879

Gnomad4 ASJ

AF:

0.914

Gnomad4 EAS

AF:

0.909

Gnomad4 SAS

AF:

0.692

Gnomad4 FIN

AF:

0.908

Gnomad4 NFE

AF:

0.862

Gnomad4 OTH

AF:

0.835

Alfa

AF:

0.833

Hom.:

2738

Bravo

AF:

0.829

Asia WGS

AF:

0.799

AC:

2778

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.4

DANN

Benign

0.34

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