rs1761987

chr10-28808141-T-C

Variant summary

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

The NR_120652.1(LINC01517):n.541T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,288 control chromosomes in the GnomAD database, including 555 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 0.082 (554 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: LINC01517 NR_120652.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65

Genes affected

LINC01517 (HGNC:51212): (long intergenic non-protein coding RNA 1517)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01517	NR_120652.1	n.541T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01517	ENST00000646289.1	n.602+64034T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12482 AN: 152128 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0967

GnomAD4 exome AF: 0.119 AC: 5 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.111 AC XY: 4 AN XY: 36

Gnomad4 AFR exome AF: 0.167

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0819 AC: 12471 AN: 152246 Hom.: 554 Cov.: 32 AF XY: 0.0791 AC XY: 5890 AN XY: 74454

Gnomad4 AFR AF: 0.0489

Gnomad4 AMR AF: 0.0784

Gnomad4 ASJ AF: 0.0981

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.0912 Hom.: 126

Bravo AF: 0.0804

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	13
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1761987; hg19: chr10-29097070;