Variant rs1406314 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 0.845 in 152,164 control chromosomes in the GnomAD database, including 55,023 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 0.84 ( 55023 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.128

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=-0.96).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.897 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:

0.845

AC:

128482

AN:

152046

Hom.:

54984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.703

Gnomad AMI

AF:

0.887

Gnomad AMR

AF:

0.909

Gnomad ASJ

AF:

0.868

Gnomad EAS

AF:

0.899

Gnomad SAS

AF:

0.808

Gnomad FIN

AF:

0.905

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.904

Gnomad OTH

AF:

0.861

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

GnomAD4 genome

AF:

0.845

AC:

128577

AN:

152164

Hom.:

55023

Cov.:

AF XY:

0.846

AC XY:

62906

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.704

Gnomad4 AMR

AF:

0.909

Gnomad4 ASJ

AF:

0.868

Gnomad4 EAS

AF:

0.899

Gnomad4 SAS

AF:

0.807

Gnomad4 FIN

AF:

0.905

Gnomad4 NFE

AF:

0.903

Gnomad4 OTH

AF:

0.863

Alfa

AF:

0.875

Hom.:

5599

Bravo

AF:

0.841

Asia WGS

AF:

0.816

AC:

2840

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.81

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