rs2334499

Variant names:

• chr11-1675619-C-T
• rs2334499
• ENST00000848993.1:n.120+2400C>T

Variant summary

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

The ENST00000848993.1(LINC02708):​n.120+2400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,084 control chromosomes in the GnomAD database, including 11,046 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 0.35 (11046 hom., cov: 32)
• Consequence: LINC02708 ENST00000848993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 83 publications found

Genes affected

LINC02708 (HGNC:54225): (long intergenic non-protein coding RNA 2708)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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
LINC02708	ENST00000848993.1	n.120+2400C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52599 AN: 151966 Hom.: 11045 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.346 AC: 52612 AN: 152084 Hom.: 11046 Cov.: 32 AF XY: 0.349 AC XY: 25939 AN XY: 74336

African (AFR) AF: 0.130 AC: 5381 AN: 41488

American (AMR) AF: 0.413 AC: 6311 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3468

East Asian (EAS) AF: 0.804 AC: 4156 AN: 5170

South Asian (SAS) AF: 0.292 AC: 1404 AN: 4812

European-Finnish (FIN) AF: 0.425 AC: 4487 AN: 10570

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28249 AN: 67986

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.397 Hom.: 17000

Bravo AF: 0.345

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.71
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2334499; hg19: chr11-1696849;