Variant rs2190736 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 0.179 in 110,771 control chromosomes in the GnomAD database, including 1,885 homozygotes. There are 5,863 hemizygotes in GnomAD. 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 0.18 ( 1885 hom., 5863 hem., cov: 22)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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:

0.179

AC:

19858

AN:

110720

Hom.:

1889

Cov.:

AF XY:

0.177

AC XY:

5854

AN XY:

32992

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.0599

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.0958

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.0985

Gnomad MID

AF:

0.0882

Gnomad NFE

AF:

0.0682

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.179

AC:

19853

AN:

110771

Hom.:

1885

Cov.:

AF XY:

0.177

AC XY:

5863

AN XY:

33053

show subpopulations

Gnomad4 AFR

AF:

0.326

Gnomad4 AMR

AF:

0.285

Gnomad4 ASJ

AF:

0.0958

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.0985

Gnomad4 NFE

AF:

0.0682

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.0207

Hom.:

Bravo

AF:

0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.80

DANN

Benign

0.28

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