rs1691943

Variant names:

• chr10-28871907-A-G
• rs1691943
• ENST00000375520.4:n.353-1349A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-28871907-A-G
• chr10-28871907-A-T

Variant summary

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

The ENST00000375520.4(LINC01517):​n.353-1349A>G 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 152,194 control chromosomes in the GnomAD database, including 54,674 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 (54674 hom., cov: 33)
• Consequence: LINC01517 ENST00000375520.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf126	NR_164114.1	n.353-1349A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01517	ENST00000375520.4	n.353-1349A>G		intron_variant	Intron 3 of 4	1
LINC01517	ENST00000614533.3	n.175-1349A>G		intron_variant	Intron 2 of 3	5
LINC01517	ENST00000643204.1	n.627-1349A>G		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128763 AN: 152076 Hom.: 54635 Cov.: 33

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.827

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: 128852 AN: 152194 Hom.: 54674 Cov.: 33 AF XY: 0.846 AC XY: 62963 AN XY: 74402

African (AFR) AF: 0.798 AC: 33125 AN: 41488

American (AMR) AF: 0.877 AC: 13422 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4234 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3997 AN: 4832

European-Finnish (FIN) AF: 0.861 AC: 9123 AN: 10592

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

European-Non Finnish (NFE) AF: 0.869 AC: 59108 AN: 68022

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

Alfa AF: 0.860 Hom.: 9099

Bravo AF: 0.846

Asia WGS AF: 0.775 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	12
DANN	Benign	0.38
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs1691943; hg19: chr10-29160836;