10-28801677-G-A

Variant names:

• chr10-28801677-G-A
• rs10826519
• ENST00000426922.6:n.290-110G>A

Variant summary

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

The NR_120652.1(LINC01517):​n.198-4370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,176 control chromosomes in the GnomAD database, including 17,448 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 0.44 (17427 hom., cov: 32)
  • Exomes 𝑓: 0.59 (21 hom.)
• Consequence: LINC01517 NR_120652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 2 publications found

Genes affected

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

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 = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120652.1. 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
	LINC01517	NR_120652.1		n.198-4370G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01517	ENST00000426922.6	TSL:5	n.290-110G>A		intron	N/A
	LINC01517	ENST00000616194.4	TSL:5	n.425-110G>A		intron	N/A
	LINC01517	ENST00000621861.1	TSL:5	n.631-4370G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67061 AN: 151942 Hom.: 17428 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.586 AC: 68 AN: 116 Hom.: 21 AF XY: 0.598 AC XY: 49 AN XY: 82

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.563 AC: 9 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.593 AC: 51 AN: 86

Other (OTH) AF: 0.500 AC: 5 AN: 10

GnomAD4 genome AF: 0.441 AC: 67060 AN: 152060 Hom.: 17427 Cov.: 32 AF XY: 0.443 AC XY: 32894 AN XY: 74294

African (AFR) AF: 0.146 AC: 6053 AN: 41496

American (AMR) AF: 0.465 AC: 7101 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1990 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3201 AN: 5172

South Asian (SAS) AF: 0.525 AC: 2528 AN: 4818

European-Finnish (FIN) AF: 0.515 AC: 5427 AN: 10532

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39125 AN: 67972

Other (OTH) AF: 0.476 AC: 1004 AN: 2110

Alfa AF: 0.504 Hom.: 5250

Bravo AF: 0.423

Asia WGS AF: 0.552 AC: 1920 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	0.34
DANN	Benign	0.51
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10826519; hg19: chr10-29090606;