Variant rs2893102 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 0.333 in 152,098 control chromosomes in the GnomAD database, including 8,788 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 0.33 ( 8788 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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:

0.333

AC:

50537

AN:

151980

Hom.:

8771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.323

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

GnomAD4 genome

AF:

0.333

AC:

50592

AN:

152098

Hom.:

8788

Cov.:

AF XY:

0.339

AC XY:

25221

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.519

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.327

Alfa

AF:

0.286

Hom.:

3250

Bravo

AF:

0.326

Asia WGS

AF:

0.518

AC:

1799

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.81

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