ENST00000446002.1:n.48-268A>G

Variant names:

• chr1-218915586-T-C
• rs10495113
• ENST00000446002.1:n.48-268A>G

Variant summary

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

The ENST00000446002.1(LINC01710):​n.48-268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 152,342 control chromosomes in the GnomAD database, including 295 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 0.024 (295 hom., cov: 33)
• Consequence: LINC01710 ENST00000446002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01710	NR_146917.1		n.98-268A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01710	ENST00000446002.1	TSL:5	n.48-268A>G		intron	N/A
	LINC01710	ENST00000655362.1		n.491-268A>G		intron	N/A
	LYPLAL1-DT	ENST00000811048.1		n.579-18486A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3615 AN: 152224 Hom.: 292 Cov.: 33

Gnomad AFR AF: 0.00779

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00688

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0238 AC: 3633 AN: 152342 Hom.: 295 Cov.: 33 AF XY: 0.0272 AC XY: 2030 AN XY: 74498

African (AFR) AF: 0.00781 AC: 325 AN: 41592

American (AMR) AF: 0.0350 AC: 535 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1595 AN: 5174

South Asian (SAS) AF: 0.108 AC: 520 AN: 4830

European-Finnish (FIN) AF: 0.00358 AC: 38 AN: 10624

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00689 AC: 469 AN: 68032

Other (OTH) AF: 0.0397 AC: 84 AN: 2116

Alfa AF: 0.0155 Hom.: 31

Bravo AF: 0.0259

Asia WGS AF: 0.205 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs10495113; hg19: chr1-219088928;