rs1942880

Variant names:

• chr18-60125977-C-T
• rs1942880
• ENST00000588794.1:n.190+755C>T

Variant summary

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

The ENST00000588794.1(LINC03111):​n.190+755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,932 control chromosomes in the GnomAD database, including 11,017 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 0.37 (11017 hom., cov: 32)
• Consequence: LINC03111 ENST00000588794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 18 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03111	NR_186639.1	n.190+755C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03111	ENST00000588794.1	n.190+755C>T		intron_variant	Intron 1 of 2	3
LINC03111	ENST00000668793.1	n.84+755C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55527 AN: 151814 Hom.: 10996 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.366 AC: 55590 AN: 151932 Hom.: 11017 Cov.: 32 AF XY: 0.361 AC XY: 26808 AN XY: 74236

African (AFR) AF: 0.511 AC: 21185 AN: 41422

American (AMR) AF: 0.293 AC: 4466 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 882 AN: 3464

East Asian (EAS) AF: 0.172 AC: 891 AN: 5172

South Asian (SAS) AF: 0.412 AC: 1978 AN: 4802

European-Finnish (FIN) AF: 0.267 AC: 2813 AN: 10550

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22220 AN: 67948

Other (OTH) AF: 0.355 AC: 750 AN: 2112

Alfa AF: 0.339 Hom.: 28477

Bravo AF: 0.371

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.21
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1942880; hg19: chr18-57793209;