Variant 10-120283977-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 0.0203 in 151,828 control chromosomes in the GnomAD database, including 217 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 0.020 ( 217 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

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=-0.9).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.120283977C>T	intergenic_region
LOC105378515	XR_001747605.1 linkuse as main transcript	n.625-4413C>T	intron_variant
LOC105378515	XR_001747606.1 linkuse as main transcript	n.916-4413C>T	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0202

AC:

3067

AN:

151712

Hom.:

212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00218

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.0741

Gnomad FIN

AF:

0.00850

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00296

Gnomad OTH

AF:

0.0197

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

GnomAD4 genome

AF:

0.0203

AC:

3083

AN:

151828

Hom.:

217

Cov.:

AF XY:

0.0240

AC XY:

1778

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.0702

Gnomad4 ASJ

AF:

0.00778

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.0737

Gnomad4 FIN

AF:

0.00850

Gnomad4 NFE

AF:

0.00296

Gnomad4 OTH

AF:

0.0247

Alfa

AF:

0.0151

Hom.:

Bravo

AF:

0.0259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.13

DANN

Benign

0.50

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