7-20954872-A-G

Variant names:

• chr7-20954872-A-G
• rs12155172
• ENST00000447262.2:n.152-65996A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447262.2(LINC01162):​n.152-65996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,160 control chromosomes in the GnomAD database, including 50,329 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 0.81 (50329 hom., cov: 31)
• Consequence: LINC01162 ENST00000447262.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 64 publications found

Genes affected

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

ENSG00000285592 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.152-65996A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2	n.152-65996A>G		intron_variant	Intron 2 of 5	5
LINC01162	ENST00000661032.1	n.207-5808A>G		intron_variant	Intron 2 of 8
LINC01162	ENST00000742942.1	n.257-5808A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123402 AN: 152042 Hom.: 50275 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.812 AC: 123516 AN: 152160 Hom.: 50329 Cov.: 31 AF XY: 0.811 AC XY: 60331 AN XY: 74388

African (AFR) AF: 0.875 AC: 36342 AN: 41514

American (AMR) AF: 0.857 AC: 13105 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3854 AN: 5174

South Asian (SAS) AF: 0.801 AC: 3858 AN: 4818

European-Finnish (FIN) AF: 0.765 AC: 8101 AN: 10596

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52751 AN: 67986

Other (OTH) AF: 0.833 AC: 1757 AN: 2110

Alfa AF: 0.789 Hom.: 191253

Bravo AF: 0.823

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
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs12155172; hg19: chr7-20994491;