rs13397583

Variant names:

• chr2-23383159-C-T
• rs13397583
• NR_187213.1:n.4160G>A

Variant summary

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

The NR_187213.1(LINC02923):​n.4160G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,208 control chromosomes in the GnomAD database, including 6,401 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 0.28 (6401 hom., cov: 32)
• Consequence: LINC02923 NR_187213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 2 publications found

Genes affected

LINC02923 (HGNC:55672): (long intergenic non-protein coding RNA 2923)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02923	NR_187213.1	n.4160G>A		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42834 AN: 152090 Hom.: 6402 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.281 AC: 42831 AN: 152208 Hom.: 6401 Cov.: 32 AF XY: 0.278 AC XY: 20688 AN XY: 74416

African (AFR) AF: 0.219 AC: 9104 AN: 41536

American (AMR) AF: 0.220 AC: 3362 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3470

East Asian (EAS) AF: 0.108 AC: 557 AN: 5180

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4824

European-Finnish (FIN) AF: 0.324 AC: 3431 AN: 10602

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22666 AN: 67972

Other (OTH) AF: 0.262 AC: 553 AN: 2114

Alfa AF: 0.316 Hom.: 5878

Bravo AF: 0.265

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.052
DANN	Benign	0.30
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs13397583; hg19: chr2-23606030;