Variant rs2413030 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 0.352 in 151,974 control chromosomes in the GnomAD database, including 10,646 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 ( 10646 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0500

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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:

0.352

AC:

53494

AN:

151856

Hom.:

10618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.352

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

GnomAD4 genome

AF:

0.352

AC:

53562

AN:

151974

Hom.:

10646

Cov.:

AF XY:

0.363

AC XY:

26944

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.220

Gnomad4 EAS

AF:

0.776

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.353

Alfa

AF:

0.271

Hom.:

1102

Bravo

AF:

0.363

Asia WGS

AF:

0.628

AC:

2181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.2

DANN

Benign

0.79

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