Variant rs1369887 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 0.721 in 152,056 control chromosomes in the GnomAD database, including 39,690 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 0.72 ( 39690 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.207

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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:

0.721

AC:

109526

AN:

151938

Hom.:

39653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.868

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.606

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.754

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.703

Gnomad OTH

AF:

0.694

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

GnomAD4 genome

AF:

0.721

AC:

109622

AN:

152056

Hom.:

39690

Cov.:

AF XY:

0.721

AC XY:

53594

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.769

Gnomad4 AMR

AF:

0.702

Gnomad4 ASJ

AF:

0.732

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.754

Gnomad4 NFE

AF:

0.703

Gnomad4 OTH

AF:

0.694

Alfa

AF:

0.692

Hom.:

17010

Bravo

AF:

0.723

Asia WGS

AF:

0.602

AC:

2096

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

6.6

DANN

Benign

0.46

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