13-99579319-T-G

Variant names:

• chr13-99579319-T-G
• rs2793772
• ENST00000437113.2:n.450+680T>G

Variant summary

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

The ENST00000437113.2(LINC01039):​n.450+680T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,914 control chromosomes in the GnomAD database, including 35,350 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 0.68 (35350 hom., cov: 30)
• Consequence: LINC01039 ENST00000437113.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01039	NR_126390.1	n.450+680T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01039	ENST00000437113.2	n.450+680T>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103118 AN: 151796 Hom.: 35334 Cov.: 30

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.679 AC: 103176 AN: 151914 Hom.: 35350 Cov.: 30 AF XY: 0.688 AC XY: 51089 AN XY: 74266

African (AFR) AF: 0.630 AC: 26061 AN: 41350

American (AMR) AF: 0.759 AC: 11577 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3470

East Asian (EAS) AF: 0.883 AC: 4567 AN: 5172

South Asian (SAS) AF: 0.694 AC: 3344 AN: 4818

European-Finnish (FIN) AF: 0.765 AC: 8084 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45115 AN: 67970

Other (OTH) AF: 0.692 AC: 1458 AN: 2108

Alfa AF: 0.690 Hom.: 6368

Bravo AF: 0.678

Asia WGS AF: 0.786 AC: 2734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2793772; hg19: chr13-100231573;