rs13166814

Positions:

• chr5-118002058-G-A
• chr5-118002058-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104997.1(LINC02147):​n.170+76927G>A variant causes a intron, non coding transcript 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 NR_104997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02147	NR_104997.1	n.170+76927G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02147	ENST00000509367.2	n.276+76927G>A		intron_variant, non_coding_transcript_variant		2
LINC02208	ENST00000660173.1	n.741-994C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0430

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.0939

Alfa AF: 0.119 Hom.: 1190

Bravo AF: 0.0842

Asia WGS AF: 0.0210 AC: 73 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13166814; hg19: chr5-117337753;