Variant rs2105183 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 0.311 in 109,947 control chromosomes in the GnomAD database, including 4,227 homozygotes. There are 10,140 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 0.31 ( 4227 hom., 10140 hem., cov: 22)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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:

0.311

AC:

34214

AN:

109893

Hom.:

4237

Cov.:

AF XY:

0.314

AC XY:

10121

AN XY:

32249

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.479

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.531

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.311

AC:

34215

AN:

109947

Hom.:

4227

Cov.:

AF XY:

0.314

AC XY:

10140

AN XY:

32313

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.479

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.753

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.217

Gnomad4 NFE

AF:

0.301

Gnomad4 OTH

AF:

0.352

Alfa

AF:

0.335

Hom.:

5588

Bravo

AF:

0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.024

DANN

Benign

0.42

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