11-115893327-C-T

Variant names:

• chr11-115893327-C-T
• rs638882
• ENST00000816384.1:n.300-722C>T

Variant summary

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

The ENST00000816384.1(ENSG00000306231):​n.300-722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,994 control chromosomes in the GnomAD database, including 16,303 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 0.46 (16303 hom., cov: 32)
• Consequence: ENSG00000306231 ENST00000816384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 8 publications found

Genes affected

ENSG00000306231 (HGNC:):

LINC02698 (HGNC:54212): (long intergenic non-protein coding RNA 2698)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02698	XR_001748394.3	n.469-7409C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306231	ENST00000816384.1	n.300-722C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70078 AN: 151876 Hom.: 16280 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.462 AC: 70146 AN: 151994 Hom.: 16303 Cov.: 32 AF XY: 0.461 AC XY: 34254 AN XY: 74290

African (AFR) AF: 0.484 AC: 20054 AN: 41414

American (AMR) AF: 0.569 AC: 8699 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2316 AN: 5174

South Asian (SAS) AF: 0.387 AC: 1868 AN: 4826

European-Finnish (FIN) AF: 0.394 AC: 4156 AN: 10548

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29877 AN: 67960

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.449 Hom.: 27676

Bravo AF: 0.480

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0080
DANN	Benign	0.37
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs638882; hg19: chr11-115764045;