ENST00000446002.1:n.47+167T>C

Variant names:

• chr1-218915971-A-G
• rs11118175
• ENST00000446002.1:n.47+167T>C

Variant summary

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

The ENST00000446002.1(LINC01710):​n.47+167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,186 control chromosomes in the GnomAD database, including 1,331 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 0.12 (1331 hom., cov: 32)
• Consequence: LINC01710 ENST00000446002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 publications found

Genes affected

LINC01710 (HGNC:52498): (long intergenic non-protein coding RNA 1710)

LYPLAL1-DT (HGNC:50560): (LYPLAL1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446002.1. 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
	LINC01710	NR_146917.1		n.97+167T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01710	ENST00000446002.1	TSL:5	n.47+167T>C		intron	N/A
	LINC01710	ENST00000655362.1		n.490+167T>C		intron	N/A
	LYPLAL1-DT	ENST00000811048.1		n.579-18871T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18331 AN: 152068 Hom.: 1329 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0823

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.121 AC: 18346 AN: 152186 Hom.: 1331 Cov.: 32 AF XY: 0.120 AC XY: 8936 AN XY: 74398

African (AFR) AF: 0.201 AC: 8329 AN: 41496

American (AMR) AF: 0.133 AC: 2037 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 285 AN: 3464

East Asian (EAS) AF: 0.128 AC: 662 AN: 5174

South Asian (SAS) AF: 0.146 AC: 703 AN: 4830

European-Finnish (FIN) AF: 0.0748 AC: 793 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5232 AN: 68024

Other (OTH) AF: 0.0935 AC: 197 AN: 2108

Alfa AF: 0.0880 Hom.: 1325

Bravo AF: 0.128

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.21
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

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: rs11118175;

hg19: chr1-219089313;