rs2716040

Positions:

• chr11-109752543-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662064.1(LINC02715):​n.304-5924A>T variant causes a intron, non coding transcript 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 ENST00000662064.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02715	ENST00000662064.1	n.304-5924A>T		intron_variant, non_coding_transcript_variant
LINC02715	ENST00000534252.2	n.543-1024A>T		intron_variant, non_coding_transcript_variant		3
LINC02715	ENST00000667432.1	n.414-5924A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.0733

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.0561

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.0936

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2716040; hg19: chr11-109623269;