rs10516117

Variant names:

• chr5-174515062-G-A
• rs10516117
• ENST00000504512.5:n.309-9000G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000504512.5(LINC01411):​n.309-9000G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,196 control chromosomes in the GnomAD database, including 615 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 0.067 (615 hom., cov: 33)
• Consequence: LINC01411 ENST00000504512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45

Genes affected

LINC01411 (HGNC:50703): (long intergenic non-protein coding RNA 1411)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01411	NR_125806.1	n.336-2697G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000504512.5	n.309-9000G>A		intron_variant	Intron 1 of 2	3
LINC01411	ENST00000507361.5	n.336-2697G>A		intron_variant	Intron 2 of 3	3
LINC01411	ENST00000510234.5	n.195-2697G>A		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10150 AN: 152078 Hom.: 615 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.00981

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0668 AC: 10160 AN: 152196 Hom.: 615 Cov.: 33 AF XY: 0.0699 AC XY: 5200 AN XY: 74416

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.00981

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0803

Alfa AF: 0.0427 Hom.: 190

Bravo AF: 0.0794

Asia WGS AF: 0.162 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516117; hg19: chr5-173942065;