Variant rs254893 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 151,916 control chromosomes in the GnomAD database, including 3,682 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 ( 3682 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577

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=-0.64).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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:

0.209

AC:

31726

AN:

151796

Hom.:

3681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.244

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.209

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

GnomAD4 genome

AF:

0.209

AC:

31725

AN:

151916

Hom.:

3682

Cov.:

AF XY:

0.209

AC XY:

15494

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.221

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.240

Hom.:

6131

Bravo

AF:

0.203

Asia WGS

AF:

0.151

AC:

525

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.81

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