Variant 2-176657649-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 0.475 in 152,114 control chromosomes in the GnomAD database, including 19,592 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 0.47 ( 19592 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.689

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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.176657649C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC01117	ENST00000652227.1 linkuse as main transcript	n.494+1871C>T	intron_variant
LINC01117	ENST00000702503.1 linkuse as main transcript	n.369+18076C>T	intron_variant
LINC01117	ENST00000702732.1 linkuse as main transcript	n.346+18076C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.475

AC:

72188

AN:

151996

Hom.:

19581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.848

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.592

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.563

Gnomad OTH

AF:

0.485

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

GnomAD4 genome

AF:

0.475

AC:

72208

AN:

152114

Hom.:

19592

Cov.:

AF XY:

0.477

AC XY:

35439

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.631

Gnomad4 ASJ

AF:

0.530

Gnomad4 EAS

AF:

0.847

Gnomad4 SAS

AF:

0.354

Gnomad4 FIN

AF:

0.592

Gnomad4 NFE

AF:

0.563

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.551

Hom.:

41435

Bravo

AF:

0.474

Asia WGS

AF:

0.603

AC:

2097

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.79

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