Variant rs1398193 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 0.826 in 152,112 control chromosomes in the GnomAD database, including 53,355 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 0.83 ( 53355 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.528

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 (NFE) allele frequency at 95% confidence interval = 0.933 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:

0.826

AC:

125580

AN:

151994

Hom.:

53330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.959

Gnomad AMR

AF:

0.809

Gnomad ASJ

AF:

0.869

Gnomad EAS

AF:

0.808

Gnomad SAS

AF:

0.853

Gnomad FIN

AF:

0.908

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.939

Gnomad OTH

AF:

0.848

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

GnomAD4 genome

AF:

0.826

AC:

125650

AN:

152112

Hom.:

53355

Cov.:

AF XY:

0.824

AC XY:

61232

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.617

Gnomad4 AMR

AF:

0.809

Gnomad4 ASJ

AF:

0.869

Gnomad4 EAS

AF:

0.808

Gnomad4 SAS

AF:

0.853

Gnomad4 FIN

AF:

0.908

Gnomad4 NFE

AF:

0.939

Gnomad4 OTH

AF:

0.850

Alfa

AF:

0.875

Hom.:

7368

Bravo

AF:

0.809

Asia WGS

AF:

0.843

AC:

2932

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.43

DANN

Benign

0.37

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