ENST00000662064.1:n.441+20G>A

Variant names:

• chr11-109744932-C-T
• rs875430
• ENST00000662064.1:n.441+20G>A

Variant summary

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

The ENST00000662064.1(LINC02715):​n.441+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,246 control chromosomes in the GnomAD database, including 619 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 0.084 (619 hom., cov: 33)
• Consequence: LINC02715 ENST00000662064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662064.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02715	NR_187367.1		n.557+20G>A		intron	N/A
	LINC02715	NR_187368.1		n.421+20G>A		intron	N/A
	LINC02715	NR_187369.1		n.612+20G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02715	ENST00000662064.1		n.441+20G>A		intron	N/A
	LINC02715	ENST00000667432.1		n.551+20G>A		intron	N/A
	LINC02715	ENST00000818760.1		n.408+59004G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12755 AN: 152128 Hom.: 619 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0838 AC: 12762 AN: 152246 Hom.: 619 Cov.: 33 AF XY: 0.0805 AC XY: 5991 AN XY: 74452

African (AFR) AF: 0.116 AC: 4836 AN: 41518

American (AMR) AF: 0.0779 AC: 1192 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4824

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10608

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0824 AC: 5601 AN: 68012

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0845 Hom.: 927

Bravo AF: 0.0885

Asia WGS AF: 0.0260 AC: 93 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.36
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs875430; hg19: chr11-109615658;