ENST00000503580.1:n.88-17522C>T

Variant names:

• chr4-188663199-C-T
• rs7686384
• ENST00000503580.1:n.88-17522C>T

Variant summary

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

The ENST00000503580.1(LINC01060):​n.88-17522C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,038 control chromosomes in the GnomAD database, including 3,293 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 0.21 (3293 hom., cov: 32)
• Consequence: LINC01060 ENST00000503580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 3 publications found

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503580.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01060	ENST00000503580.1	TSL:3	n.88-17522C>T		intron	N/A
	LINC01060	ENST00000664177.2		n.338-17084C>T		intron	N/A
	LINC01060	ENST00000692519.2		n.389-17084C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31576 AN: 151920 Hom.: 3285 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.208 AC: 31616 AN: 152038 Hom.: 3293 Cov.: 32 AF XY: 0.203 AC XY: 15061 AN XY: 74332

African (AFR) AF: 0.231 AC: 9575 AN: 41472

American (AMR) AF: 0.184 AC: 2809 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3472

East Asian (EAS) AF: 0.167 AC: 863 AN: 5172

South Asian (SAS) AF: 0.204 AC: 981 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10550

Middle Eastern (MID) AF: 0.262 AC: 76 AN: 290

European-Non Finnish (NFE) AF: 0.212 AC: 14413 AN: 67958

Other (OTH) AF: 0.225 AC: 474 AN: 2106

Alfa AF: 0.208 Hom.: 12919

Bravo AF: 0.206

Asia WGS AF: 0.196 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.0
DANN	Benign	0.59
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs7686384; hg19: chr4-189584353;