rs952044

Variant names:

• chr18-60130878-C-T
• rs952044
• ENST00000588794.1:n.346+1223C>T

Variant summary

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

The ENST00000588794.1(LINC03111):​n.346+1223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,810 control chromosomes in the GnomAD database, including 9,491 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 0.34 (9491 hom., cov: 31)
• Consequence: LINC03111 ENST00000588794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 12 publications found

Genes affected

LINC03111 (HGNC:56850): (long intergenic non-protein coding RNA 3111)

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 (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03111	NR_186639.1	n.346+1223C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03111	ENST00000588794.1	n.346+1223C>T		intron_variant	Intron 2 of 2	3
LINC03111	ENST00000668793.1	n.240+1223C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52260 AN: 151692 Hom.: 9483 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.345 AC: 52299 AN: 151810 Hom.: 9491 Cov.: 31 AF XY: 0.340 AC XY: 25232 AN XY: 74190

African (AFR) AF: 0.440 AC: 18184 AN: 41366

American (AMR) AF: 0.286 AC: 4348 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 886 AN: 3464

East Asian (EAS) AF: 0.173 AC: 894 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4808

European-Finnish (FIN) AF: 0.267 AC: 2810 AN: 10532

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22236 AN: 67936

Other (OTH) AF: 0.338 AC: 714 AN: 2114

Alfa AF: 0.352 Hom.: 3541

Bravo AF: 0.347

Asia WGS AF: 0.244 AC: 848 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.86
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs952044; hg19: chr18-57798110;