Variant rs2281517 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 0.209 in 152,174 control chromosomes in the GnomAD database, including 3,617 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 0.21 ( 3616 hom., cov: 32)

Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.415

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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:

0.209

AC:

31729

AN:

152050

Hom.:

3607

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.362

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.213

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.209

AC:

31756

AN:

152168

Hom.:

3616

Cov.:

AF XY:

0.211

AC XY:

15699

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.212

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.204

Hom.:

297

Bravo

AF:

0.197

Asia WGS

AF:

0.344

AC:

1196

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.5

DANN

Benign

0.63

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