Variant rs7754552 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 0.89 in 152,046 control chromosomes in the GnomAD database, including 60,994 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 0.89 ( 60994 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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:

0.890

AC:

135266

AN:

151928

Hom.:

60955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.728

Gnomad AMI

AF:

0.911

Gnomad AMR

AF:

0.929

Gnomad ASJ

AF:

0.927

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.961

Gnomad FIN

AF:

0.986

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.949

Gnomad OTH

AF:

0.907

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

GnomAD4 genome

AF:

0.890

AC:

135363

AN:

152046

Hom.:

60994

Cov.:

AF XY:

0.894

AC XY:

66454

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.728

Gnomad4 AMR

AF:

0.929

Gnomad4 ASJ

AF:

0.927

Gnomad4 EAS

AF:

0.997

Gnomad4 SAS

AF:

0.961

Gnomad4 FIN

AF:

0.986

Gnomad4 NFE

AF:

0.949

Gnomad4 OTH

AF:

0.907

Alfa

AF:

0.915

Hom.:

7509

Bravo

AF:

0.876

Asia WGS

AF:

0.956

AC:

3325

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.27

DANN

Benign

0.30

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