rs17118741

Variant names:

• chr11-115742253-G-A
• rs17118741
• ENST00000539305.2:n.681+65472G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-115742253-G-A
• chr11-115742253-G-T

Variant summary

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

The ENST00000539305.2(LINC02698):​n.681+65472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,142 control chromosomes in the GnomAD database, including 3,094 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 0.17 (3094 hom., cov: 32)
• Consequence: LINC02698 ENST00000539305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 4 publications found

Genes affected

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

ENSG00000288020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02698	XR_001748394.3	n.468+65472G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02698	ENST00000539305.2	n.681+65472G>A		intron_variant	Intron 2 of 2	4
ENSG00000288020	ENST00000670874.1	n.38+7368G>A		intron_variant	Intron 1 of 3
ENSG00000288020	ENST00000763598.1	n.65+7368G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26504 AN: 152024 Hom.: 3071 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.175 AC: 26572 AN: 152142 Hom.: 3094 Cov.: 32 AF XY: 0.183 AC XY: 13617 AN XY: 74382

African (AFR) AF: 0.307 AC: 12745 AN: 41494

American (AMR) AF: 0.108 AC: 1647 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1409 AN: 5148

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4810

European-Finnish (FIN) AF: 0.213 AC: 2261 AN: 10594

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6633 AN: 68004

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.111 Hom.: 1351

Bravo AF: 0.170

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.035
DANN	Benign	0.54
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17118741; hg19: chr11-115612971;