Variant rs1023890 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 0.552 in 151,762 control chromosomes in the GnomAD database, including 25,162 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 0.55 ( 25162 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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:

0.552

AC:

83660

AN:

151644

Hom.:

25114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.555

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

GnomAD4 genome

AF:

0.552

AC:

83770

AN:

151762

Hom.:

25162

Cov.:

AF XY:

0.551

AC XY:

40857

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.807

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.416

Gnomad4 NFE

AF:

0.426

Gnomad4 OTH

AF:

0.556

Alfa

AF:

0.494

Hom.:

3248

Bravo

AF:

0.580

Asia WGS

AF:

0.508

AC:

1759

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.1

DANN

Benign

0.69

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