11-116649810-G-T

Variant names:

• chr11-116649810-G-T
• rs1240773
• ENST00000439483.3:n.114-3088G>T

Variant summary

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

The ENST00000439483.3(LINC02702):​n.114-3088G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,160 control chromosomes in the GnomAD database, including 3,444 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 0.21 (3444 hom., cov: 32)
• Consequence: LINC02702 ENST00000439483.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 8 publications found

Genes affected

LINC02702 (HGNC:54217): (long intergenic non-protein coding RNA 2702)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02702	NR_135069.1	n.117-3088G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02702	ENST00000439483.3	n.114-3088G>T		intron_variant	Intron 1 of 3	2
LINC02702	ENST00000444123.6	n.117-3088G>T		intron_variant	Intron 1 of 2	5
LINC02702	ENST00000665087.1	n.31-3088G>T		intron_variant	Intron 1 of 2
LINC02702	ENST00000669244.1	n.77-3088G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31595 AN: 152042 Hom.: 3437 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.208 AC: 31627 AN: 152160 Hom.: 3444 Cov.: 32 AF XY: 0.207 AC XY: 15364 AN XY: 74398

African (AFR) AF: 0.165 AC: 6846 AN: 41508

American (AMR) AF: 0.223 AC: 3413 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5188

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4810

European-Finnish (FIN) AF: 0.181 AC: 1913 AN: 10592

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15015 AN: 67982

Other (OTH) AF: 0.248 AC: 522 AN: 2108

Alfa AF: 0.218 Hom.: 11097

Bravo AF: 0.206

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.34
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1240773; hg19: chr11-116520527;