Variant rs7242459 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 0.345 in 152,078 control chromosomes in the GnomAD database, including 10,085 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 0.35 ( 10085 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0840

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=-0.66).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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:

0.345

AC:

52476

AN:

151960

Hom.:

10092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.357

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

GnomAD4 genome

AF:

0.345

AC:

52475

AN:

152078

Hom.:

10085

Cov.:

AF XY:

0.343

AC XY:

25480

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.344

Gnomad4 ASJ

AF:

0.434

Gnomad4 EAS

AF:

0.237

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.435

Gnomad4 OTH

AF:

0.353

Alfa

AF:

0.273

Hom.:

768

Bravo

AF:

0.330

Asia WGS

AF:

0.266

AC:

926

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.7

DANN

Benign

0.90

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