13-29882170-C-T

Variant names:

• chr13-29882170-C-T
• rs1590501
• ENST00000453470.2:n.377+5859G>A

Variant summary

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

The ENST00000453470.2(LINC00297):​n.377+5859G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,084 control chromosomes in the GnomAD database, including 37,415 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 0.70 (37415 hom., cov: 33)
• Consequence: LINC00297 ENST00000453470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 2 publications found

Genes affected

LINC00297 (HGNC:39210): (long intergenic non-protein coding RNA 297)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453470.2. 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
	LINC00297	NR_046510.1		n.377+5859G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00297	ENST00000453470.2	TSL:2	n.377+5859G>A		intron	N/A
	LINC00297	ENST00000768376.1		n.301-1144G>A		intron	N/A
	LINC00297	ENST00000768377.1		n.409-1144G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105994 AN: 151966 Hom.: 37372 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.698 AC: 106088 AN: 152084 Hom.: 37415 Cov.: 33 AF XY: 0.698 AC XY: 51881 AN XY: 74354

African (AFR) AF: 0.704 AC: 29196 AN: 41464

American (AMR) AF: 0.709 AC: 10833 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2903 AN: 3470

East Asian (EAS) AF: 0.918 AC: 4758 AN: 5182

South Asian (SAS) AF: 0.788 AC: 3802 AN: 4822

European-Finnish (FIN) AF: 0.572 AC: 6044 AN: 10562

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45997 AN: 67978

Other (OTH) AF: 0.742 AC: 1570 AN: 2116

Alfa AF: 0.690 Hom.: 16952

Bravo AF: 0.711

Asia WGS AF: 0.848 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1590501; hg19: chr13-30456307;