rs2716040

Variant names:

• chr11-109752543-T-A
• rs2716040
• ENST00000534252.2:n.543-1024A>T

Variant summary

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

The ENST00000534252.2(LINC02715):​n.543-1024A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,246 control chromosomes in the GnomAD database, including 580 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 0.083 (580 hom., cov: 32)
• Consequence: LINC02715 ENST00000534252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02715	NR_187367.1	n.420-5924A>T		intron_variant	Intron 2 of 4
LINC02715	NR_187368.1	n.284-5924A>T		intron_variant	Intron 2 of 4
LINC02715	NR_187369.1	n.475-5924A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02715	ENST00000534252.2	n.543-1024A>T		intron_variant	Intron 4 of 4	3
LINC02715	ENST00000662064.1	n.304-5924A>T		intron_variant	Intron 2 of 4
LINC02715	ENST00000667432.1	n.414-5924A>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12559 AN: 152128 Hom.: 579 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0825 AC: 12565 AN: 152246 Hom.: 580 Cov.: 32 AF XY: 0.0796 AC XY: 5924 AN XY: 74446

African (AFR) AF: 0.0836 AC: 3474 AN: 41538

American (AMR) AF: 0.0733 AC: 1121 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0520 AC: 251 AN: 4824

European-Finnish (FIN) AF: 0.0561 AC: 595 AN: 10614

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6496 AN: 68000

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.0867 Hom.: 66

Bravo AF: 0.0839

Asia WGS AF: 0.0250 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2716040; hg19: chr11-109623269;