Genetic Variant LINC01473:n.104+73326A>G (chr2-186349003-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000667056.1(LINC01473):n.104+73326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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

LINC01473
ENST00000667056.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.325

Publications

2 publications found

Variant links:

Genes affected

LINC01473 (HGNC:51109): (long intergenic non-protein coding RNA 1473)

LINC01473 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01473	ENST00000667056.1 link	n.104+73326A>G	intron_variant	Intron 1 of 9
LINC01473	ENST00000668985.2 link	n.405-43784A>G	intron_variant	Intron 2 of 10
LINC01473	ENST00000671599.1 link	n.104+73326A>G	intron_variant	Intron 1 of 6

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

African (AFR)

AF:

0.156

AC:

6452

AN:

41470

American (AMR)

AF:

0.138

AC:

2105

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

677

AN:

3470

East Asian (EAS)

AF:

0.100

AC:

518

AN:

5182

South Asian (SAS)

AF:

0.191

AC:

921

AN:

4820

European-Finnish (FIN)

AF:

0.247

AC:

2610

AN:

10574

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.189

AC:

12869

AN:

67986

Other (OTH)

AF:

0.181

AC:

381

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1129

2258

3387

4516

5645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.178

Hom.:

3167

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

(source)

DANN

Benign

0.84

PhyloP100

0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over