Variant rs1833219 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 0.709 in 152,012 control chromosomes in the GnomAD database, including 38,427 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 0.71 ( 38427 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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:

0.709

AC:

107760

AN:

151894

Hom.:

38414

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.814

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.717

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.751

Gnomad FIN

AF:

0.697

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.728

Gnomad OTH

AF:

0.708

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

GnomAD4 genome

AF:

0.709

AC:

107823

AN:

152012

Hom.:

38427

Cov.:

AF XY:

0.709

AC XY:

52666

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.699

Gnomad4 ASJ

AF:

0.717

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.751

Gnomad4 FIN

AF:

0.697

Gnomad4 NFE

AF:

0.728

Gnomad4 OTH

AF:

0.707

Alfa

AF:

0.631

Hom.:

1831

Bravo

AF:

0.707

Asia WGS

AF:

0.762

AC:

2652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.8

DANN

Benign

0.82

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