ENST00000509367.2:n.276+76927G>A

Variant names:

• chr5-118002058-G-A
• rs13166814
• ENST00000509367.3:n.302+76927G>A

Variant summary

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

The ENST00000509367.3(LINC02147):​n.302+76927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 151,930 control chromosomes in the GnomAD database, including 877 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 0.090 (877 hom., cov: 32)
• Consequence: LINC02147 ENST00000509367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 7 publications found

Genes affected

LINC02147 (HGNC:53007): (long intergenic non-protein coding RNA 2147)

LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509367.3. 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
	LINC02147	NR_104997.1		n.170+76927G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02147	ENST00000509367.3	TSL:2	n.302+76927G>A		intron	N/A
	LINC02147	ENST00000509669.1	TSL:3	n.254+6321G>A		intron	N/A
	LINC02147	ENST00000657852.1		n.267+76927G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13606 AN: 151812 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0949

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

GnomAD4 genome AF: 0.0895 AC: 13604 AN: 151930 Hom.: 877 Cov.: 32 AF XY: 0.0844 AC XY: 6269 AN XY: 74238

African (AFR) AF: 0.0241 AC: 1001 AN: 41504

American (AMR) AF: 0.0719 AC: 1096 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3468

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5144

South Asian (SAS) AF: 0.0430 AC: 207 AN: 4814

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10560

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9590 AN: 67882

Other (OTH) AF: 0.0939 AC: 198 AN: 2108

Alfa AF: 0.113 Hom.: 2272

Bravo AF: 0.0842

Asia WGS AF: 0.0210 AC: 73 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.42
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13166814; hg19: chr5-117337753;