Variant rs1291183 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 0.638 in 151,768 control chromosomes in the GnomAD database, including 31,569 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 0.64 ( 31569 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.441

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=-0.61).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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:

0.638

AC:

96730

AN:

151648

Hom.:

31537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.721

Gnomad ASJ

AF:

0.709

Gnomad EAS

AF:

0.663

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.748

Gnomad NFE

AF:

0.688

Gnomad OTH

AF:

0.668

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

GnomAD4 genome

AF:

0.638

AC:

96803

AN:

151768

Hom.:

31569

Cov.:

AF XY:

0.637

AC XY:

47240

AN XY:

74132

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.721

Gnomad4 ASJ

AF:

0.709

Gnomad4 EAS

AF:

0.663

Gnomad4 SAS

AF:

0.733

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.688

Gnomad4 OTH

AF:

0.673

Alfa

AF:

0.688

Hom.:

49614

Bravo

AF:

0.637

Asia WGS

AF:

0.720

AC:

2502

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.53

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