rs10518306

Variant names:

• chr4-123815050-C-T
• rs10518306
• ENST00000515769.1:n.113-14045C>T

Variant summary

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

The ENST00000515769.1(LINC01091):​n.113-14045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 152,088 control chromosomes in the GnomAD database, including 763 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 0.093 (763 hom., cov: 32)
• Consequence: LINC01091 ENST00000515769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 5 publications found

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515769.1. 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
	LINC01091	NR_027105.3		n.537-14045C>T		intron	N/A
	LINC01091	NR_027106.2		n.113-14045C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	ENST00000515769.1	TSL:1	n.113-14045C>T		intron	N/A
	LINC01091	ENST00000508111.6	TSL:5	n.492-14045C>T		intron	N/A
	LINC01091	ENST00000511919.6	TSL:3	n.563-14045C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14144 AN: 151968 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0931 AC: 14152 AN: 152088 Hom.: 763 Cov.: 32 AF XY: 0.0922 AC XY: 6854 AN XY: 74348

African (AFR) AF: 0.0570 AC: 2364 AN: 41494

American (AMR) AF: 0.0754 AC: 1151 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.0539 AC: 279 AN: 5176

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1512 AN: 10560

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7867 AN: 67982

Other (OTH) AF: 0.111 AC: 234 AN: 2112

Alfa AF: 0.103 Hom.: 189

Bravo AF: 0.0867

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10518306; hg19: chr4-124736205;