Variant 13-105547179-G-T 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 0.707 in 151,924 control chromosomes in the GnomAD database, including 39,897 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 0.71 ( 39897 hom., cov: 30)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.105547179G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107358

AN:

151808

Hom.:

39885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.822

Gnomad AMR

AF:

0.846

Gnomad ASJ

AF:

0.841

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.703

Gnomad FIN

AF:

0.808

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.749

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

GnomAD4 genome

AF:

0.707

AC:

107407

AN:

151924

Hom.:

39897

Cov.:

AF XY:

0.711

AC XY:

52784

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.463

Gnomad4 AMR

AF:

0.846

Gnomad4 ASJ

AF:

0.841

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.703

Gnomad4 FIN

AF:

0.808

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.749

Alfa

AF:

0.791

Hom.:

48131

Bravo

AF:

0.702

Asia WGS

AF:

0.658

AC:

2287

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.074

DANN

Benign

0.59

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