ENST00000818760.1:n.1313G>A

Variant names:

• chr11-109306090-C-T
• rs655763
• ENST00000818760.1:n.1313G>A

Variant summary

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

The ENST00000818760.1(LINC02715):​n.1313G>A 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 0.585 in 151,934 control chromosomes in the GnomAD database, including 27,145 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 0.59 (27145 hom., cov: 31)
• Consequence: LINC02715 ENST00000818760.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 3 publications found

Genes affected

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818760.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02715	ENST00000818760.1		n.1313G>A		non_coding_transcript_exon	Exon 10 of 10
	LINC02715	ENST00000818766.1		n.196+2145G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88907 AN: 151816 Hom.: 27151 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.585 AC: 88921 AN: 151934 Hom.: 27145 Cov.: 31 AF XY: 0.585 AC XY: 43436 AN XY: 74254

African (AFR) AF: 0.422 AC: 17474 AN: 41384

American (AMR) AF: 0.534 AC: 8158 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2028 AN: 3466

East Asian (EAS) AF: 0.506 AC: 2601 AN: 5136

South Asian (SAS) AF: 0.626 AC: 3019 AN: 4820

European-Finnish (FIN) AF: 0.735 AC: 7768 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45920 AN: 67980

Other (OTH) AF: 0.568 AC: 1201 AN: 2116

Alfa AF: 0.627 Hom.: 38671

Bravo AF: 0.564

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs655763; hg19: chr11-109176817;