Variant 1-192827775-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 0.726 in 152,096 control chromosomes in the GnomAD database, including 40,242 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 0.73 ( 40242 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.991

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.192827775C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285280	ENST00000644058.1 linkuse as main transcript	n.194-61581G>A	intron_variant
ENSG00000285280	ENST00000644134.1 linkuse as main transcript	n.105-61581G>A	intron_variant
ENSG00000285280	ENST00000645822.1 linkuse as main transcript	n.142-814G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.726

AC:

110332

AN:

151978

Hom.:

40206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.760

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.812

Gnomad FIN

AF:

0.662

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.739

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

GnomAD4 genome

AF:

0.726

AC:

110423

AN:

152096

Hom.:

40242

Cov.:

AF XY:

0.730

AC XY:

54253

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.722

Gnomad4 AMR

AF:

0.746

Gnomad4 ASJ

AF:

0.760

Gnomad4 EAS

AF:

0.876

Gnomad4 SAS

AF:

0.813

Gnomad4 FIN

AF:

0.662

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.741

Alfa

AF:

0.631

Hom.:

2731

Bravo

AF:

0.732

Asia WGS

AF:

0.834

AC:

2895

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

DANN

Benign

0.26

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