Variant rs1708403 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 0.571 in 151,786 control chromosomes in the GnomAD database, including 25,894 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 0.57 ( 25894 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.134467612G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

86632

AN:

151668

Hom.:

25855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.750

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.514

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.523

Gnomad OTH

AF:

0.546

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

GnomAD4 genome

AF:

0.571

AC:

86723

AN:

151786

Hom.:

25894

Cov.:

AF XY:

0.564

AC XY:

41857

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.750

Gnomad4 AMR

AF:

0.463

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.514

Gnomad4 FIN

AF:

0.418

Gnomad4 NFE

AF:

0.523

Gnomad4 OTH

AF:

0.545

Alfa

AF:

0.381

Hom.:

863

Bravo

AF:

0.586

Asia WGS

AF:

0.534

AC:

1855

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

DANN

Benign

0.48

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