rs1373877

Variant names:

• chr12-64982742-T-C
• rs1373877
• ENST00000649369.1:n.270-316T>C

Variant summary

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

The ENST00000649369.1(LINC02389):​n.270-316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,008 control chromosomes in the GnomAD database, including 14,719 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 0.43 (14719 hom., cov: 32)
• Consequence: LINC02389 ENST00000649369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

LINC02389 (HGNC:53316): (long intergenic non-protein coding RNA 2389)

LINC02231 (HGNC:53100): (long intergenic non-protein coding RNA 2231)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02231	NR_146276.1	n.16-220A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02389	ENST00000649369.1	n.270-316T>C		intron_variant	Intron 2 of 4
LINC02389	ENST00000653132.1	n.242-316T>C		intron_variant	Intron 2 of 4
LINC02389	ENST00000653818.1	n.127-316T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65797 AN: 151888 Hom.: 14726 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.433 AC: 65809 AN: 152008 Hom.: 14719 Cov.: 32 AF XY: 0.429 AC XY: 31872 AN XY: 74300

African (AFR) AF: 0.409 AC: 16942 AN: 41450

American (AMR) AF: 0.417 AC: 6369 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3468

East Asian (EAS) AF: 0.106 AC: 550 AN: 5170

South Asian (SAS) AF: 0.343 AC: 1656 AN: 4826

European-Finnish (FIN) AF: 0.467 AC: 4918 AN: 10542

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31970 AN: 67952

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.463 Hom.: 46104

Bravo AF: 0.432

Asia WGS AF: 0.272 AC: 947 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.92
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1373877; hg19: chr12-65376522;