rs1165640

Variant names:

• chr3-193820202-C-T
• rs1165640
• ENST00000837985.1:n.326-1032G>A

Variant summary

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

The ENST00000837985.1(LINC02038):​n.326-1032G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,194 control chromosomes in the GnomAD database, including 58,212 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 0.87 (58212 hom., cov: 33)
• Consequence: LINC02038 ENST00000837985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

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.326-1032G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132822 AN: 152076 Hom.: 58175 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.873 AC: 132914 AN: 152194 Hom.: 58212 Cov.: 33 AF XY: 0.874 AC XY: 65000 AN XY: 74404

African (AFR) AF: 0.810 AC: 33628 AN: 41510

American (AMR) AF: 0.863 AC: 13197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3803 AN: 5174

South Asian (SAS) AF: 0.921 AC: 4430 AN: 4812

European-Finnish (FIN) AF: 0.924 AC: 9796 AN: 10598

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61976 AN: 68032

Other (OTH) AF: 0.867 AC: 1827 AN: 2108

Alfa AF: 0.897 Hom.: 200961

Bravo AF: 0.863

Asia WGS AF: 0.816 AC: 2833 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.71
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1165640; hg19: chr3-193537991;