10-28871947-A-G

Variant names:

• chr10-28871947-A-G
• rs1775933
• ENST00000375520.4:n.353-1309A>G

Variant summary

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

The ENST00000375520.4(LINC01517):​n.353-1309A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,202 control chromosomes in the GnomAD database, including 54,790 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 (54790 hom., cov: 33)
• Consequence: LINC01517 ENST00000375520.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444
• 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=-0.88).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf126	NR_164114.1		n.353-1309A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01517	ENST00000375520.4	TSL:1	n.353-1309A>G		intron	N/A
	LINC01517	ENST00000614533.3	TSL:5	n.175-1309A>G		intron	N/A
	LINC01517	ENST00000643204.1		n.627-1309A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128909 AN: 152084 Hom.: 54751 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.853

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: 0.848 AC: 128998 AN: 152202 Hom.: 54790 Cov.: 33 AF XY: 0.848 AC XY: 63065 AN XY: 74412

African (AFR) AF: 0.799 AC: 33158 AN: 41508

American (AMR) AF: 0.877 AC: 13428 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2973 AN: 3466

East Asian (EAS) AF: 0.819 AC: 4229 AN: 5162

South Asian (SAS) AF: 0.853 AC: 4113 AN: 4824

European-Finnish (FIN) AF: 0.861 AC: 9122 AN: 10596

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

European-Non Finnish (NFE) AF: 0.869 AC: 59107 AN: 68020

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

Alfa AF: 0.860 Hom.: 9514

Bravo AF: 0.847

Asia WGS AF: 0.783 AC: 2721 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.43
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1775933; hg19: chr10-29160876;