Variant rs2548145 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 0.552 in 151,696 control chromosomes in the GnomAD database, including 24,141 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 0.55 ( 24141 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.216

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 = 0.783 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:

0.552

AC:

83710

AN:

151576

Hom.:

24093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.676

Gnomad AMI

AF:

0.554

Gnomad AMR

AF:

0.617

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.804

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.530

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

GnomAD4 genome

AF:

0.552

AC:

83812

AN:

151696

Hom.:

24141

Cov.:

AF XY:

0.553

AC XY:

40977

AN XY:

74108

show subpopulations

Gnomad4 AFR

AF:

0.676

Gnomad4 AMR

AF:

0.618

Gnomad4 ASJ

AF:

0.436

Gnomad4 EAS

AF:

0.803

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.464

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.534

Alfa

AF:

0.494

Hom.:

30126

Bravo

AF:

0.576

Asia WGS

AF:

0.626

AC:

2180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

DANN

Benign

0.48

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