10-28808141-T-C

Variant names:

• chr10-28808141-T-C
• rs1761987
• ENST00000426922.6:n.902T>C

Variant summary

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

The ENST00000426922.6(LINC01517):​n.902T>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 ENST00000426922.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65
• Publications: 0 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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426922.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01517	NR_120652.1		n.541T>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01517	ENST00000426922.6	TSL:5	n.902T>C		non_coding_transcript_exon	Exon 6 of 6
	LINC01517	ENST00000655545.1		n.892T>C		non_coding_transcript_exon	Exon 6 of 6
	LINC01517	ENST00000660375.1		n.490T>C		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.107 AC: 3 AN: 28

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.0489 AC: 2030 AN: 41554

American (AMR) AF: 0.0784 AC: 1199 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0981 AC: 340 AN: 3466

East Asian (EAS) AF: 0.0516 AC: 267 AN: 5174

South Asian (SAS) AF: 0.0762 AC: 368 AN: 4830

European-Finnish (FIN) AF: 0.0590 AC: 626 AN: 10606

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7301 AN: 68008

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.0904 Hom.: 128

Bravo AF: 0.0804

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs1761987; hg19: chr10-29097070;