13-29884600-G-T

Variant names:

• chr13-29884600-G-T
• rs9314986
• ENST00000453470.2:n.377+3429C>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+3429C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,106 control chromosomes in the GnomAD database, including 36,701 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 0.69 (36701 hom., cov: 32)
• Consequence: LINC00297 ENST00000453470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 14 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=-0.9).
• 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+3429C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00297	ENST00000453470.2	TSL:2	n.377+3429C>A		intron	N/A
	LINC00297	ENST00000768376.1		n.300+3429C>A		intron	N/A
	LINC00297	ENST00000768377.1		n.408+3429C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104946 AN: 151988 Hom.: 36656 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.691 AC: 105043 AN: 152106 Hom.: 36701 Cov.: 32 AF XY: 0.691 AC XY: 51366 AN XY: 74336

African (AFR) AF: 0.677 AC: 28099 AN: 41498

American (AMR) AF: 0.706 AC: 10795 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2907 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4766 AN: 5192

South Asian (SAS) AF: 0.806 AC: 3887 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6032 AN: 10556

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

European-Non Finnish (NFE) AF: 0.677 AC: 46009 AN: 67964

Other (OTH) AF: 0.739 AC: 1560 AN: 2112

Alfa AF: 0.699 Hom.: 76184

Bravo AF: 0.703

Asia WGS AF: 0.853 AC: 2967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-0.059

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9314986;

hg19: chr13-30458737;