rs2716045

Variant names:

• chr11-109724918-A-G
• rs2716045
• ENST00000818760.1:n.408+79018T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-109724918-A-G
• chr11-109724918-A-T

Variant summary

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

The ENST00000818760.1(LINC02715):​n.408+79018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,140 control chromosomes in the GnomAD database, including 42,972 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 0.74 (42972 hom., cov: 32)
• Consequence: LINC02715 ENST00000818760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02715	ENST00000818760.1	n.408+79018T>C		intron_variant	Intron 3 of 9
LINC02715	ENST00000818761.1	n.169+79018T>C		intron_variant	Intron 2 of 3
LINC02715	ENST00000818762.1	n.147+79018T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112329 AN: 152024 Hom.: 42910 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.739 AC: 112448 AN: 152140 Hom.: 42972 Cov.: 32 AF XY: 0.740 AC XY: 55054 AN XY: 74380

African (AFR) AF: 0.936 AC: 38859 AN: 41534

American (AMR) AF: 0.755 AC: 11532 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3896 AN: 5180

South Asian (SAS) AF: 0.614 AC: 2955 AN: 4814

European-Finnish (FIN) AF: 0.702 AC: 7412 AN: 10564

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43291 AN: 67978

Other (OTH) AF: 0.708 AC: 1493 AN: 2110

Alfa AF: 0.660 Hom.: 60016

Bravo AF: 0.756

Asia WGS AF: 0.651 AC: 2267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.70
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2716045; hg19: chr11-109595644; COSMIC: COSV69481450;