rs17306391

Variant names:

• chr11-23169826-A-C
• rs17306391
• ENST00000533591.1:n.268+3213A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-23169826-A-C
• chr11-23169826-A-G

Variant summary

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

The ENST00000533591.1(LINC02718):​n.268+3213A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 151,936 control chromosomes in the GnomAD database, including 243 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 0.047 (243 hom., cov: 32)
• Consequence: LINC02718 ENST00000533591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

Genes affected

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02718	NR_187205.1	n.1450+3034A>C		intron_variant	Intron 10 of 13
LINC02718	NR_187206.1	n.1246+3034A>C		intron_variant	Intron 9 of 11
LINC02718	NR_187207.1	n.1349+3034A>C		intron_variant	Intron 10 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02718	ENST00000533591.1	n.268+3213A>C		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7204 AN: 151818 Hom.: 243 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.000970

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0474 AC: 7199 AN: 151936 Hom.: 243 Cov.: 32 AF XY: 0.0448 AC XY: 3327 AN XY: 74272

African (AFR) AF: 0.0136 AC: 564 AN: 41522

American (AMR) AF: 0.0530 AC: 806 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 208 AN: 3464

East Asian (EAS) AF: 0.000972 AC: 5 AN: 5144

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4822

European-Finnish (FIN) AF: 0.0346 AC: 367 AN: 10610

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0729 AC: 4948 AN: 67866

Other (OTH) AF: 0.0599 AC: 126 AN: 2104

Alfa AF: 0.0419 Hom.: 119

Bravo AF: 0.0488

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-1.8
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: rs17306391; hg19: chr11-23191372;