Variant rs4825172 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 0.303 in 110,037 control chromosomes in the GnomAD database, including 3,863 homozygotes. There are 9,787 hemizygotes in GnomAD. 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 0.30 ( 3863 hom., 9787 hem., cov: 22)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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:

0.303

AC:

33278

AN:

109994

Hom.:

3855

Cov.:

AF XY:

0.303

AC XY:

9779

AN XY:

32284

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.317

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

GnomAD4 genome

AF:

0.303

AC:

33294

AN:

110037

Hom.:

3863

Cov.:

AF XY:

0.303

AC XY:

9787

AN XY:

32337

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.375

Gnomad4 ASJ

AF:

0.356

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.326

Alfa

AF:

0.341

Hom.:

9140

Bravo

AF:

0.295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.18

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