10-28870419-G-T

Variant names:

• chr10-28870419-G-T
• rs1775929
• ENST00000375520.4:n.353-2837G>T

Variant summary

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

The ENST00000375520.4(LINC01517):​n.353-2837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,182 control chromosomes in the GnomAD database, including 54,777 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 0.85 (54777 hom., cov: 32)
• Consequence: LINC01517 ENST00000375520.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

Genes affected

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

C10orf126 (HGNC:28693): (chromosome 10 open reading frame 126)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375520.4. 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
	C10orf126	NR_164114.1		n.353-2837G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01517	ENST00000375520.4	TSL:1	n.353-2837G>T		intron	N/A
	LINC01517	ENST00000614533.3	TSL:5	n.175-2837G>T		intron	N/A
	LINC01517	ENST00000643204.1		n.627-2837G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128883 AN: 152064 Hom.: 54738 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.847 AC: 128972 AN: 152182 Hom.: 54777 Cov.: 32 AF XY: 0.848 AC XY: 63058 AN XY: 74404

African (AFR) AF: 0.799 AC: 33131 AN: 41488

American (AMR) AF: 0.877 AC: 13416 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2973 AN: 3468

East Asian (EAS) AF: 0.819 AC: 4237 AN: 5174

South Asian (SAS) AF: 0.853 AC: 4111 AN: 4822

European-Finnish (FIN) AF: 0.861 AC: 9126 AN: 10600

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59108 AN: 68020

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.860 Hom.: 9516

Bravo AF: 0.847

Asia WGS AF: 0.783 AC: 2723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1775929; hg19: chr10-29159348;