11-82817778-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

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 = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526305.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02734	NR_183631.1		n.*37C>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02734	ENST00000526305.2	TSL:2	n.*39C>T		downstream_gene	N/A
	LINC02734	ENST00000657980.2		n.*37C>T		downstream_gene	N/A

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

African (AFR) AF: 0.283 AC: 11710 AN: 41440

American (AMR) AF: 0.0436 AC: 666 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4820

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0325 AC: 2213 AN: 68006

Other (OTH) AF: 0.0831 AC: 175 AN: 2106

Alfa AF: 0.0513 Hom.: 1729

Bravo AF: 0.108

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs7108762; hg19: chr11-82528820;