Variant rs1928007 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 0.839 in 151,922 control chromosomes in the GnomAD database, including 54,250 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 0.84 ( 54250 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0180

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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:

0.839

AC:

127323

AN:

151806

Hom.:

54203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.911

Gnomad AMR

AF:

0.880

Gnomad ASJ

AF:

0.839

Gnomad EAS

AF:

0.955

Gnomad SAS

AF:

0.880

Gnomad FIN

AF:

0.932

Gnomad MID

AF:

0.783

Gnomad NFE

AF:

0.903

Gnomad OTH

AF:

0.837

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

GnomAD4 genome

AF:

0.839

AC:

127424

AN:

151922

Hom.:

54250

Cov.:

AF XY:

0.841

AC XY:

62440

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.880

Gnomad4 ASJ

AF:

0.839

Gnomad4 EAS

AF:

0.955

Gnomad4 SAS

AF:

0.879

Gnomad4 FIN

AF:

0.932

Gnomad4 NFE

AF:

0.903

Gnomad4 OTH

AF:

0.839

Alfa

AF:

0.869

Hom.:

7970

Bravo

AF:

0.827

Asia WGS

AF:

0.910

AC:

3122

AN:

3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.2

DANN

Benign

0.30

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