Variant rs258415 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 0.239 in 152,134 control chromosomes in the GnomAD database, including 5,227 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 0.24 ( 5227 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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:

0.239

AC:

36385

AN:

152016

Hom.:

5216

Cov.:

show subpopulations

Gnomad AFR

AF:

0.402

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.239

AC:

36429

AN:

152134

Hom.:

5227

Cov.:

AF XY:

0.235

AC XY:

17491

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.402

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.269

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.135

Gnomad4 NFE

AF:

0.182

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.195

Hom.:

1441

Bravo

AF:

0.249

Asia WGS

AF:

0.202

AC:

701

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.24

DANN

Benign

0.38

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