13-99581376-T-G

Variant names:

• chr13-99581376-T-G
• rs1104973
• NR_126390.1:n.647+1011T>G

Variant summary

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

The NR_126390.1(LINC01039):​n.647+1011T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,018 control chromosomes in the GnomAD database, including 34,550 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 0.67 (34550 hom., cov: 32)
• Consequence: LINC01039 NR_126390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 3 publications found

Genes affected

LINC01039 (HGNC:49027): (long intergenic non-protein coding RNA 1039)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126390.1. 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
	LINC01039	NR_126390.1		n.647+1011T>G		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101851 AN: 151898 Hom.: 34534 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.670 AC: 101909 AN: 152018 Hom.: 34550 Cov.: 32 AF XY: 0.679 AC XY: 50482 AN XY: 74326

African (AFR) AF: 0.601 AC: 24919 AN: 41446

American (AMR) AF: 0.755 AC: 11526 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3468

East Asian (EAS) AF: 0.880 AC: 4550 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3342 AN: 4820

European-Finnish (FIN) AF: 0.766 AC: 8106 AN: 10588

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45054 AN: 67958

Other (OTH) AF: 0.687 AC: 1445 AN: 2104

Alfa AF: 0.662 Hom.: 17781

Bravo AF: 0.668

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.59
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1104973; hg19: chr13-100233630;