Variant rs7552167 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 0.867 in 152,248 control chromosomes in the GnomAD database, including 57,281 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 0.87 ( 57281 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.586

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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.894 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:

0.867

AC:

131851

AN:

152130

Hom.:

57229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.898

Gnomad AMR

AF:

0.906

Gnomad ASJ

AF:

0.845

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.747

Gnomad NFE

AF:

0.859

Gnomad OTH

AF:

0.855

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

GnomAD4 genome

AF:

0.867

AC:

131957

AN:

152248

Hom.:

57281

Cov.:

AF XY:

0.866

AC XY:

64497

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.889

Gnomad4 AMR

AF:

0.906

Gnomad4 ASJ

AF:

0.845

Gnomad4 EAS

AF:

0.759

Gnomad4 SAS

AF:

0.884

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.859

Gnomad4 OTH

AF:

0.845

Alfa

AF:

0.863

Hom.:

117696

Bravo

AF:

0.873

Asia WGS

AF:

0.780

AC:

2712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.69

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