Variant rs222916 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 0.181 in 152,054 control chromosomes in the GnomAD database, including 2,553 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 0.18 ( 2553 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

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 (SAS) allele frequency at 95% confidence interval = 0.229 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:

0.181

AC:

27453

AN:

151938

Hom.:

2549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.186

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

GnomAD4 genome

AF:

0.181

AC:

27482

AN:

152054

Hom.:

2553

Cov.:

AF XY:

0.179

AC XY:

13285

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.191

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.118

Hom.:

220

Bravo

AF:

0.174

Asia WGS

AF:

0.165

AC:

575

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

5.2

DANN

Benign

0.74

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