Variant 2-186349003-T-C 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 0.176 in 152,078 control chromosomes in the GnomAD database, including 2,408 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 0.18 ( 2408 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.325

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 (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.186349003T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC01473	ENST00000667056.1 linkuse as main transcript	n.104+73326A>G	intron_variant
LINC01473	ENST00000671599.1 linkuse as main transcript	n.104+73326A>G	intron_variant
LINC01473	ENST00000703419.1 linkuse as main transcript	n.344-43784A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26716

AN:

151960

Hom.:

2400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.176

AC:

26718

AN:

152078

Hom.:

2408

Cov.:

AF XY:

0.179

AC XY:

13313

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.195

Gnomad4 EAS

AF:

0.100

Gnomad4 SAS

AF:

0.191

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.189

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.179

Hom.:

2744

Bravo

AF:

0.164

Asia WGS

AF:

0.163

AC:

565

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.6

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