Variant rs2256902 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 0.133 in 433,556 control chromosomes in the GnomAD database, including 4,540 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 0.15 ( 2086 hom., cov: 33)

Exomes 𝑓: 0.12 ( 2454 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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:

0.152

AC:

23113

AN:

152118

Hom.:

2075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.123

AC:

34491

AN:

281320

Hom.:

2454

AF XY:

0.123

AC XY:

17825

AN XY:

145068

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.223

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.0900

Gnomad4 NFE exome

AF:

0.107

Gnomad4 OTH exome

AF:

0.133

GnomAD4 genome

AF:

0.152

AC:

23165

AN:

152236

Hom.:

2086

Cov.:

AF XY:

0.151

AC XY:

11259

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.216

Gnomad4 ASJ

AF:

0.131

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.0802

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.120

Hom.:

1147

Bravo

AF:

0.166

Asia WGS

AF:

0.157

AC:

546

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.6

DANN

Benign

0.56

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