Variant rs1479067 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 0.732 in 151,866 control chromosomes in the GnomAD database, including 40,902 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 0.73 ( 40902 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.101814850C>A	intergenic_region
LOC105379102	XR_007058891.1 linkuse as main transcript	n.294+807G>T	intron_variant
LOC105379102	XR_948628.3 linkuse as main transcript	n.294+807G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.732

AC:

111034

AN:

151748

Hom.:

40858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.804

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.659

Gnomad EAS

AF:

0.808

Gnomad SAS

AF:

0.773

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.750

Gnomad OTH

AF:

0.721

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

GnomAD4 genome

AF:

0.732

AC:

111132

AN:

151866

Hom.:

40902

Cov.:

AF XY:

0.737

AC XY:

54718

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.660

Gnomad4 AMR

AF:

0.794

Gnomad4 ASJ

AF:

0.659

Gnomad4 EAS

AF:

0.807

Gnomad4 SAS

AF:

0.773

Gnomad4 FIN

AF:

0.773

Gnomad4 NFE

AF:

0.750

Gnomad4 OTH

AF:

0.719

Alfa

AF:

0.743

Hom.:

25011

Bravo

AF:

0.731

Asia WGS

AF:

0.792

AC:

2753

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.59

DANN

Benign

0.33

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