chr5-118073397-T-C

Variant names:

• chr5-118073397-T-C
• rs2416504
• ENST00000509367.3:n.303-114068T>C

Variant summary

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

The ENST00000509367.3(LINC02147):​n.303-114068T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,718 control chromosomes in the GnomAD database, including 15,470 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 0.40 (15470 hom., cov: 30)
• Consequence: LINC02147 ENST00000509367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02147	NR_104997.1	n.170+148266T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02147	ENST00000509367.3	n.303-114068T>C		intron_variant	Intron 2 of 3	2
LINC02147	ENST00000509669.1	n.254+77660T>C		intron_variant	Intron 2 of 3	3
LINC02147	ENST00000657852.1	n.268-133323T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60666 AN: 151602 Hom.: 15461 Cov.: 30

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.400 AC: 60676 AN: 151718 Hom.: 15470 Cov.: 30 AF XY: 0.413 AC XY: 30648 AN XY: 74128

African (AFR) AF: 0.111 AC: 4590 AN: 41428

American (AMR) AF: 0.550 AC: 8346 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5038 AN: 5148

South Asian (SAS) AF: 0.587 AC: 2823 AN: 4808

European-Finnish (FIN) AF: 0.558 AC: 5854 AN: 10500

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31000 AN: 67884

Other (OTH) AF: 0.409 AC: 863 AN: 2108

Alfa AF: 0.374 Hom.: 2383

Bravo AF: 0.387

Asia WGS AF: 0.717 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2416504; hg19: chr5-117409092;