Variant rs282095 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 0.562 in 152,050 control chromosomes in the GnomAD database, including 24,337 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 0.56 ( 24337 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.738

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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:

0.563

AC:

85468

AN:

151932

Hom.:

24316

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.641

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.564

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

GnomAD4 genome

AF:

0.562

AC:

85523

AN:

152050

Hom.:

24337

Cov.:

AF XY:

0.559

AC XY:

41550

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.489

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.497

Gnomad4 FIN

AF:

0.641

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.561

Alfa

AF:

0.582

Hom.:

3193

Bravo

AF:

0.553

Asia WGS

AF:

0.423

AC:

1474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.92

DANN

Benign

0.75

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