Variant rs2249596 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 0.354 in 152,058 control chromosomes in the GnomAD database, including 9,886 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 ( 9886 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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:

0.354

AC:

53749

AN:

151938

Hom.:

9873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.405

Gnomad AMI

AF:

0.485

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.521

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.330

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

GnomAD4 genome

AF:

0.354

AC:

53794

AN:

152058

Hom.:

9886

Cov.:

AF XY:

0.357

AC XY:

26555

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.405

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.503

Gnomad4 SAS

AF:

0.519

Gnomad4 FIN

AF:

0.302

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.338

Alfa

AF:

0.313

Hom.:

5301

Bravo

AF:

0.357

Asia WGS

AF:

0.550

AC:

1911

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.47

DANN

Benign

0.62

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