dbSNP rs10713532: LINC01162:n.152-63534delG (chr7-20957333-TG-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000447262.2(LINC01162):n.152-63534delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 49314 hom., cov: 0)

Consequence

LINC01162
ENST00000447262.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

5 publications found

Variant links:

Genes affected

LINC01162 (HGNC:49528): (long intergenic non-protein coding RNA 1162)

LINC01162 links:

ENSG00000285592 (HGNC:):

ENSG00000285592 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01162	NR_126381.1 link	n.152-63533delG		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01162	ENST00000447262.2 link	n.152-63534delG	intron_variant	Intron 2 of 5	5
LINC01162	ENST00000661032.1 link	n.207-3346delG	intron_variant	Intron 2 of 8
LINC01162	ENST00000742942.1 link	n.257-3346delG	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.804

AC:

122162

AN:

151962

Hom.:

49265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.854

Gnomad AMI

AF:

0.841

Gnomad AMR

AF:

0.850

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.762

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.764

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.831

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

GnomAD4 genome

AF:

0.804

AC:

122270

AN:

152080

Hom.:

49314

Cov.:

AF XY:

0.803

AC XY:

59707

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.854

AC:

35443

AN:

41490

American (AMR)

AF:

0.850

AC:

12994

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.785

AC:

2725

AN:

3472

East Asian (EAS)

AF:

0.762

AC:

3936

AN:

5168

South Asian (SAS)

AF:

0.795

AC:

3823

AN:

4810

European-Finnish (FIN)

AF:

0.764

AC:

8079

AN:

10576

Middle Eastern (MID)

AF:

0.847

AC:

249

AN:

294

European-Non Finnish (NFE)

AF:

0.772

AC:

52505

AN:

67970

Other (OTH)

AF:

0.831

AC:

1751

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1229

2458

3688

4917

6146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.785

Hom.:

5717

Bravo

AF:

0.815

Asia WGS

AF:

0.796

AC:

2765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Splicing

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

Publications

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rs10713532

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