11-82817778-C-T

Variant names:

• chr11-82817778-C-T
• rs7108762
• ENST00000526305.2:n.*39C>T

Variant summary

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

The ENST00000526305.2(LINC02734):​n.*39C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,120 control chromosomes in the GnomAD database, including 1,749 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 0.098 (1749 hom., cov: 32)
• Consequence: LINC02734 ENST00000526305.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

LINC02734 (HGNC:54251): (long intergenic non-protein coding RNA 2734)

ACMG classification

Verdict is Benign. Variant got -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 = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02734	NR_183631.1	n.*37C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02734	ENST00000526305.2	n.*39C>T		downstream_gene_variant		2
LINC02734	ENST00000657980.1	n.*37C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14962 AN: 152004 Hom.: 1745 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0985 AC: 14980 AN: 152120 Hom.: 1749 Cov.: 32 AF XY: 0.0949 AC XY: 7063 AN XY: 74408

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00560

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0325

Gnomad4 OTH AF: 0.0831

Alfa AF: 0.0344 Hom.: 356

Bravo AF: 0.108

Asia WGS AF: 0.0180 AC: 62 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	1.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7108762; hg19: chr11-82528820;