Variant rs2215383 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 0.543 in 152,010 control chromosomes in the GnomAD database, including 22,697 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 0.54 ( 22697 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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:

0.543

AC:

82470

AN:

151890

Hom.:

22687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.543

Gnomad OTH

AF:

0.534

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

GnomAD4 genome

AF:

0.543

AC:

82522

AN:

152010

Hom.:

22697

Cov.:

AF XY:

0.539

AC XY:

40057

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.567

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.681

Gnomad4 SAS

AF:

0.624

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.543

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.545

Hom.:

2897

Bravo

AF:

0.544

Asia WGS

AF:

0.636

AC:

2205

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.1

DANN

Benign

0.60

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