Variant rs1878526 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 0.242 in 152,012 control chromosomes in the GnomAD database, including 4,742 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 ( 4742 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.493

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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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:

0.242

AC:

36694

AN:

151896

Hom.:

4728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.225

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

GnomAD4 genome

AF:

0.242

AC:

36736

AN:

152012

Hom.:

4742

Cov.:

AF XY:

0.239

AC XY:

17782

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.195

Gnomad4 EAS

AF:

0.355

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.211

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.216

Hom.:

6110

Bravo

AF:

0.246

Asia WGS

AF:

0.277

AC:

961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.74

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