rs17306391

chr11-23169826-A-Cchr11-23169826-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533591.1(LINC02718):n.268+3213A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02718	XR_007062625.1	n.1374+3034A>C		intron_variant, non_coding_transcript_variant
LINC02718	XR_007062624.1	n.12949+3034A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02718	ENST00000533591.1	n.268+3213A>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.000972

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.0599

Alfa AF: 0.0361 Hom.: 38

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17306391; hg19: chr11-23191372;