chr11-109751428-T-C

Variant names:

• chr11-109751428-T-C
• rs2099378
• ENST00000662064.1:n.304-4809A>G

Variant summary

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

The ENST00000662064.1(LINC02715):​n.304-4809A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,046 control chromosomes in the GnomAD database, including 16,854 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 0.39 (16854 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC02715 ENST00000662064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02715	NR_187367.1	n.420-4809A>G		intron_variant	Intron 2 of 4
LINC02715	NR_187368.1	n.284-4809A>G		intron_variant	Intron 2 of 4
LINC02715	NR_187369.1	n.475-4809A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02715	ENST00000662064.1	n.304-4809A>G		intron_variant	Intron 2 of 4
LINC02715	ENST00000667432.1	n.414-4809A>G		intron_variant	Intron 2 of 4
LINC02715	ENST00000818760.1	n.408+52508A>G		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59943 AN: 151924 Hom.: 16809 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.395 AC: 60048 AN: 152044 Hom.: 16854 Cov.: 32 AF XY: 0.386 AC XY: 28713 AN XY: 74328

African (AFR) AF: 0.802 AC: 33245 AN: 41434

American (AMR) AF: 0.272 AC: 4161 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1358 AN: 5172

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4812

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10590

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16380 AN: 67986

Other (OTH) AF: 0.371 AC: 783 AN: 2108

Alfa AF: 0.256 Hom.: 3317

Bravo AF: 0.420

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	10
DANN	Benign	0.45
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2099378; hg19: chr11-109622154;