Variant 10-52789608-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 0.223 in 151,850 control chromosomes in the GnomAD database, including 4,074 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 0.22 ( 4074 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.52789608C>T	intergenic_region
LOC105378306	XR_945963.2 linkuse as main transcript	n.387-590C>T	intron_variant
LOC105378307	XR_945965.3 linkuse as main transcript	n.370-5274G>A	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33880

AN:

151732

Hom.:

4077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.248

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

GnomAD4 genome

AF:

0.223

AC:

33872

AN:

151850

Hom.:

4074

Cov.:

AF XY:

0.220

AC XY:

16331

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.227

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.231

Gnomad4 NFE

AF:

0.277

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.252

Hom.:

2091

Bravo

AF:

0.212

Asia WGS

AF:

0.179

AC:

625

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.30

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