rs13398206

chr2-198304372-T-Cchr2-198304372-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110267.1(LINC01923):n.358-2556A>G variant causes a intron, non coding transcript 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 NR_110267.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01923	NR_110267.1	n.358-2556A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01923	ENST00000658157.1	n.70-2556A>G		intron_variant, non_coding_transcript_variant
LINC01923	ENST00000451266.1	n.156-2556A>G		intron_variant, non_coding_transcript_variant		4
LINC01923	ENST00000456248.1	n.75-2556A>G		intron_variant, non_coding_transcript_variant		2
PLCL1	ENST00000625084.1	n.45-50923T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.304

Alfa AF: 0.305 Hom.: 16115

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13398206; hg19: chr2-199169096;