rs10516117

Variant names:

• chr5-174515062-G-A
• rs10516117
• ENST00000758094.1:n.19C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000758094.1(ENSG00000298815):​n.19C>T 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 0.0668 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: ENSG00000298815 ENST00000758094.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• Publications: 0 publications found

Genes affected

ENSG00000298815 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000298815	ENST00000758094.1	n.19C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01411	ENST00000504512.6	n.309-9000G>A		intron_variant	Intron 1 of 6	3
LINC01411	ENST00000506862.2	n.318-2697G>A		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.0820 AC: 3405 AN: 41506

American (AMR) AF: 0.137 AC: 2099 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5158

South Asian (SAS) AF: 0.120 AC: 581 AN: 4824

European-Finnish (FIN) AF: 0.00981 AC: 104 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0310 AC: 2106 AN: 68022

Other (OTH) AF: 0.0803 AC: 170 AN: 2116

Alfa AF: 0.0479 Hom.: 305

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
PhyloP100		2.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10516117; hg19: chr5-173942065;