ENST00000447262.2:n.152-63534delG

Variant names:

• chr7-20957333-TG-T
• rs10713532
• ENST00000447262.2:n.152-63534delG

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 5 publications found

Genes affected

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

ENSG00000285592 (HGNC:58953):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447262.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01162	NR_126381.1		n.152-63533delG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01162	ENST00000447262.2	TSL:5	n.152-63534delG		intron	N/A
	LINC01162	ENST00000661032.1		n.207-3346delG		intron	N/A
	LINC01162	ENST00000742942.1		n.257-3346delG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122162 AN: 151962 Hom.: 49265 Cov.: 0

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.: 0 AF XY: 0.803 AC XY: 59707 AN XY: 74336

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10713532;

hg19: chr7-20996952;