ENST00000503580.1:n.88-14796C>T

Variant names:

• chr4-188665925-C-T
• rs7659062
• ENST00000503580.1:n.88-14796C>T

Variant summary

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

The ENST00000503580.1(LINC01060):​n.88-14796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,948 control chromosomes in the GnomAD database, including 2,068 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 0.16 (2068 hom., cov: 32)
• Consequence: LINC01060 ENST00000503580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01060	ENST00000503580.1	TSL:3	n.88-14796C>T		intron	N/A
	LINC01060	ENST00000664177.2		n.338-14358C>T		intron	N/A
	LINC01060	ENST00000692519.2		n.389-14358C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24654 AN: 151830 Hom.: 2065 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.162 AC: 24678 AN: 151948 Hom.: 2068 Cov.: 32 AF XY: 0.157 AC XY: 11683 AN XY: 74278

African (AFR) AF: 0.188 AC: 7784 AN: 41432

American (AMR) AF: 0.144 AC: 2202 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3466

East Asian (EAS) AF: 0.107 AC: 552 AN: 5164

South Asian (SAS) AF: 0.116 AC: 560 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11342 AN: 67912

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.162 Hom.: 8772

Bravo AF: 0.162

Asia WGS AF: 0.117 AC: 407 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	1.3
DANN	Benign	0.37
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7659062; hg19: chr4-189587079;