rs13398206

Variant names:

• chr2-198304372-T-C
• rs13398206
• ENST00000451266.1:n.156-2556A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-198304372-T-C
• chr2-198304372-T-G

Variant summary

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

The ENST00000456248.2(LINC01923):​n.77-2556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,028 control chromosomes in the GnomAD database, including 6,410 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 (6410 hom., cov: 31)
• Consequence: LINC01923 ENST00000456248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 9 publications found

Genes affected

LINC01923 (HGNC:52742): (long intergenic non-protein coding RNA 1923)

PLCL1 (HGNC:9063): (phospholipase C like 1 (inactive)) Predicted to enable phospholipase C activity. Predicted to be involved in negative regulation of cold-induced thermogenesis and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within several processes, including gamma-aminobutyric acid signaling pathway; regulation of GABAergic synaptic transmission; and regulation of peptidyl-serine phosphorylation. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456248.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01923	NR_110267.1		n.358-2556A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01923	ENST00000451266.1	TSL:4	n.156-2556A>G		intron	N/A
	LINC01923	ENST00000456248.2	TSL:2	n.77-2556A>G		intron	N/A
	PLCL1	ENST00000625084.1	TSL:5	n.45-50923T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43230 AN: 151910 Hom.: 6406 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.285 AC: 43255 AN: 152028 Hom.: 6410 Cov.: 31 AF XY: 0.275 AC XY: 20450 AN XY: 74316

African (AFR) AF: 0.301 AC: 12492 AN: 41462

American (AMR) AF: 0.220 AC: 3366 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3472

East Asian (EAS) AF: 0.0873 AC: 452 AN: 5176

South Asian (SAS) AF: 0.202 AC: 974 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2328 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21520 AN: 67944

Other (OTH) AF: 0.304 AC: 641 AN: 2106

Alfa AF: 0.303 Hom.: 23833

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs13398206; hg19: chr2-199169096;