Variant rs2057369 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 0.224 in 151,752 control chromosomes in the GnomAD database, including 3,918 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 0.22 ( 3918 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.640

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 (EAS) allele frequency at 95% confidence interval = 0.342 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:

0.224

AC:

33941

AN:

151634

Hom.:

3910

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.224

AC:

33987

AN:

151752

Hom.:

3918

Cov.:

AF XY:

0.227

AC XY:

16801

AN XY:

74124

show subpopulations

Gnomad4 AFR

AF:

0.227

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.355

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.210

Hom.:

1768

Bravo

AF:

0.231

Asia WGS

AF:

0.202

AC:

703

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.16

DANN

Benign

0.58

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