ENST00000446589.2:n.-138C>T

Variant names:

• chr10-128912659-C-T
• rs7085203
• ENST00000446589.2:n.-138C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000446589.2(LINC02667):​n.-138C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,160 control chromosomes in the GnomAD database, including 1,527 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 0.14 (1527 hom., cov: 33)
• Consequence: LINC02667 ENST00000446589.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 8 publications found

Genes affected

LINC02667 (HGNC:54153): (long intergenic non-protein coding RNA 2667)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446589.2. 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
	LINC02667	NR_148990.1		n.-174C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02667	ENST00000446589.2	TSL:2	n.-138C>T		upstream_gene	N/A
	LINC02667	ENST00000656262.2		n.-150C>T		upstream_gene	N/A
	LINC02667	ENST00000661127.1		n.-157C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21106 AN: 152042 Hom.: 1525 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.139 AC: 21117 AN: 152160 Hom.: 1527 Cov.: 33 AF XY: 0.138 AC XY: 10284 AN XY: 74408

African (AFR) AF: 0.160 AC: 6629 AN: 41492

American (AMR) AF: 0.117 AC: 1787 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3472

East Asian (EAS) AF: 0.145 AC: 751 AN: 5168

South Asian (SAS) AF: 0.142 AC: 683 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1071 AN: 10590

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9353 AN: 68010

Other (OTH) AF: 0.165 AC: 349 AN: 2110

Alfa AF: 0.139 Hom.: 6543

Bravo AF: 0.139

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.72
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs7085203; hg19: chr10-130710923;