11-134703916-C-T

Variant names:

• chr11-134703916-C-T
• rs11825685
• ENST00000842729.1:n.751-11791C>T

Variant summary

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

The ENST00000842729.1(LINC02706):​n.751-11791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 152,184 control chromosomes in the GnomAD database, including 602 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 0.084 (602 hom., cov: 32)
• Consequence: LINC02706 ENST00000842729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 3 publications found

Genes affected

LINC02706 (HGNC:54223): (long intergenic non-protein coding RNA 2706)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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
LINC02706	ENST00000842729.1	n.751-11791C>T		intron_variant	Intron 3 of 3
LINC02706	ENST00000842730.1	n.539-11791C>T		intron_variant	Intron 3 of 3
LINC02706	ENST00000842731.1	n.584-11791C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12753 AN: 152066 Hom.: 599 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.0839 AC: 12762 AN: 152184 Hom.: 602 Cov.: 32 AF XY: 0.0794 AC XY: 5907 AN XY: 74412

African (AFR) AF: 0.0728 AC: 3021 AN: 41512

American (AMR) AF: 0.0818 AC: 1251 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0428 AC: 206 AN: 4812

European-Finnish (FIN) AF: 0.0390 AC: 414 AN: 10608

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7245 AN: 67986

Other (OTH) AF: 0.0922 AC: 195 AN: 2114

Alfa AF: 0.0677 Hom.: 151

Bravo AF: 0.0880

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.38
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11825685; hg19: chr11-134573810;