Variant 5-107704741-C-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 0.338 in 151,858 control chromosomes in the GnomAD database, including 9,691 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 0.34 ( 9691 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.850

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=-0.65).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.107704741C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000249959	ENST00000502287.1 linkuse as main transcript	n.434-2434G>A	intron_variant	5
ENSG00000249959	ENST00000509458.5 linkuse as main transcript	n.322+461G>A	intron_variant	3
ENSG00000249959	ENST00000653896.1 linkuse as main transcript	n.130+461G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51246

AN:

151738

Hom.:

9688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.346

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

GnomAD4 genome

AF:

0.338

AC:

51258

AN:

151858

Hom.:

9691

Cov.:

AF XY:

0.340

AC XY:

25215

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.400

Gnomad4 ASJ

AF:

0.402

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.541

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.406

Gnomad4 OTH

AF:

0.342

Alfa

AF:

0.377

Hom.:

6066

Bravo

AF:

0.329

Asia WGS

AF:

0.387

AC:

1348

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

4.4

DANN

Benign

0.84

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