ENST00000583161.1:n.165-474T>C

Variant names:

• chr17-39004193-A-G
• rs1014263
• ENST00000583161.1:n.165-474T>C

Variant summary

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

The ENST00000583161.1(LINC02079):​n.165-474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,938 control chromosomes in the GnomAD database, including 1,467 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 0.10 (1467 hom., cov: 31)
• Consequence: LINC02079 ENST00000583161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 6 publications found

Genes affected

LINC02079 (HGNC:52927): (long intergenic non-protein coding RNA 2079)

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 = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02079	ENST00000583161.1	n.165-474T>C		intron_variant	Intron 2 of 2	3
LINC02079	ENST00000717160.1	n.1061-474T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15736 AN: 151818 Hom.: 1456 Cov.: 31

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 15755 AN: 151938 Hom.: 1467 Cov.: 31 AF XY: 0.110 AC XY: 8134 AN XY: 74248

African (AFR) AF: 0.0259 AC: 1073 AN: 41466

American (AMR) AF: 0.294 AC: 4476 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1570 AN: 5148

South Asian (SAS) AF: 0.146 AC: 701 AN: 4812

European-Finnish (FIN) AF: 0.0903 AC: 952 AN: 10538

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0929 AC: 6313 AN: 67982

Other (OTH) AF: 0.109 AC: 229 AN: 2104

Alfa AF: 0.106 Hom.: 3063

Bravo AF: 0.118

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1014263; hg19: chr17-37160446;