5-126192299-C-T

Variant names:

• chr5-126192299-C-T
• rs1366100
• ENST00000450613.2:n.71+87432G>A

Variant summary

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

The ENST00000450613.2(ENSG00000248752):​n.71+87432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,808 control chromosomes in the GnomAD database, including 22,997 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 0.55 (22997 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000450613.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 3 publications found

Genes affected

ENSG00000248752 (HGNC:):

LINC02039 (HGNC:52879): (long intergenic non-protein coding RNA 2039)

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 = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02039	NR_105042.1	n.266-778C>T		intron_variant	Intron 2 of 3
LOC124901056	XR_007058919.1	n.1620-94138G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000450613.2	n.71+87432G>A		intron_variant	Intron 1 of 2	3
LINC02039	ENST00000507428.2	n.266-778C>T		intron_variant	Intron 2 of 3	4
ENSG00000248752	ENST00000651847.1	n.152+2855G>A		intron_variant	Intron 2 of 15

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83083 AN: 151690 Hom.: 22990 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.548 AC: 83126 AN: 151808 Hom.: 22997 Cov.: 32 AF XY: 0.548 AC XY: 40630 AN XY: 74182

African (AFR) AF: 0.611 AC: 25286 AN: 41408

American (AMR) AF: 0.463 AC: 7053 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2908 AN: 5140

South Asian (SAS) AF: 0.569 AC: 2734 AN: 4802

European-Finnish (FIN) AF: 0.549 AC: 5784 AN: 10526

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36089 AN: 67928

Other (OTH) AF: 0.524 AC: 1101 AN: 2102

Alfa AF: 0.539 Hom.: 9204

Bravo AF: 0.539

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1366100; hg19: chr5-125527992;