rs2133890

Variant names:

• chr3-193820088-A-G
• rs2133890
• ENST00000837985.1:n.326-918T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000837985.1(LINC02038):​n.326-918T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 152,330 control chromosomes in the GnomAD database, including 14 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 0.012 (14 hom., cov: 33)
• Consequence: LINC02038 ENST00000837985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 0 publications found

Genes affected

LINC02038 (HGNC:52878): (long intergenic non-protein coding RNA 2038)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0124 (1896/152330) while in subpopulation SAS AF = 0.0207 (100/4830). AF 95% confidence interval is 0.0182. There are 14 homozygotes in GnomAd4. There are 893 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 14 gene

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
LINC02038	ENST00000837985.1	n.326-918T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0125 AC: 1898 AN: 152212 Hom.: 14 Cov.: 33

Gnomad AFR AF: 0.00311

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0124 AC: 1896 AN: 152330 Hom.: 14 Cov.: 33 AF XY: 0.0120 AC XY: 893 AN XY: 74492

African (AFR) AF: 0.00308 AC: 128 AN: 41584

American (AMR) AF: 0.0103 AC: 157 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3466

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4830

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1299 AN: 68024

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.0166 Hom.: 11

Bravo AF: 0.0117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.38
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2133890; hg19: chr3-193537877;