Variant rs2478333 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 0.244 in 152,154 control chromosomes in the GnomAD database, including 5,819 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 0.24 ( 5819 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Variant links:

Genome browser will be placed here

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 (NFE) allele frequency at 95% confidence interval = 0.354 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:

0.244

AC:

37138

AN:

152036

Hom.:

5817

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0627

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.0780

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.278

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

GnomAD4 genome

AF:

0.244

AC:

37142

AN:

152154

Hom.:

5819

Cov.:

AF XY:

0.239

AC XY:

17766

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.0626

Gnomad4 AMR

AF:

0.243

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.0776

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.280

Alfa

AF:

0.334

Hom.:

13884

Bravo

AF:

0.235

Asia WGS

AF:

0.176

AC:

614

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

5.6

DANN

Benign

0.31

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