Variant 5-113937501-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 0.181 in 152,008 control chromosomes in the GnomAD database, including 2,784 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 0.18 ( 2784 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.468

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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.113937501G>T		intergenic_region
LOC124901047	XR_007058906.1 linkuse as main transcript	n.2086-60675G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27585

AN:

151890

Hom.:

2785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.164

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

GnomAD4 genome

AF:

0.181

AC:

27587

AN:

152008

Hom.:

2784

Cov.:

AF XY:

0.186

AC XY:

13814

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.163

Alfa

AF:

0.204

Hom.:

1587

Bravo

AF:

0.168

Asia WGS

AF:

0.186

AC:

645

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.83

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