Variant rs7524281 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 0.408 in 152,032 control chromosomes in the GnomAD database, including 13,504 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 0.41 ( 13504 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.902

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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:

0.407

AC:

61892

AN:

151916

Hom.:

13478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.573

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.349

Gnomad OTH

AF:

0.391

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

GnomAD4 genome

AF:

0.408

AC:

61964

AN:

152032

Hom.:

13504

Cov.:

AF XY:

0.405

AC XY:

30089

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.574

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.286

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.349

Gnomad4 OTH

AF:

0.387

Alfa

AF:

0.350

Hom.:

12779

Bravo

AF:

0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.27

DANN

Benign

0.28

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