Variant rs2325443 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 0.7 in 151,846 control chromosomes in the GnomAD database, including 38,303 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 0.70 ( 38303 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

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=-0.62).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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:

0.700

AC:

106184

AN:

151728

Hom.:

38291

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.924

Gnomad AMR

AF:

0.767

Gnomad ASJ

AF:

0.817

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.750

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.718

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

GnomAD4 genome

AF:

0.700

AC:

106236

AN:

151846

Hom.:

38303

Cov.:

AF XY:

0.699

AC XY:

51857

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.508

Gnomad4 AMR

AF:

0.767

Gnomad4 ASJ

AF:

0.817

Gnomad4 EAS

AF:

0.811

Gnomad4 SAS

AF:

0.733

Gnomad4 FIN

AF:

0.750

Gnomad4 NFE

AF:

0.772

Gnomad4 OTH

AF:

0.717

Alfa

AF:

0.700

Hom.:

5526

Bravo

AF:

0.693

Asia WGS

AF:

0.730

AC:

2534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.50

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