ENST00000456248.2:n.77-16164A>G

Variant names:

• chr2-198317980-T-C
• rs997467
• ENST00000456248.2:n.77-16164A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000456248.2(LINC01923):​n.77-16164A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,912 control chromosomes in the GnomAD database, including 20,545 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 0.49 (20545 hom., cov: 33)
• Consequence: LINC01923 ENST00000456248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 5 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01923	NR_110267.1	n.358-16164A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01923	ENST00000456248.2	n.77-16164A>G		intron_variant	Intron 1 of 1	2
PLCL1	ENST00000625084.1	n.45-37315T>C		intron_variant	Intron 1 of 1	5
LINC01923	ENST00000658157.1	n.70-16164A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73952 AN: 151792 Hom.: 20538 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.431

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.487 AC: 73960 AN: 151912 Hom.: 20545 Cov.: 33 AF XY: 0.498 AC XY: 36990 AN XY: 74244

African (AFR) AF: 0.209 AC: 8654 AN: 41474

American (AMR) AF: 0.566 AC: 8648 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4583 AN: 5182

South Asian (SAS) AF: 0.760 AC: 3656 AN: 4810

European-Finnish (FIN) AF: 0.607 AC: 6393 AN: 10526

Middle Eastern (MID) AF: 0.418 AC: 118 AN: 282

European-Non Finnish (NFE) AF: 0.567 AC: 38512 AN: 67874

Other (OTH) AF: 0.498 AC: 1050 AN: 2110

Alfa AF: 0.541 Hom.: 22436

Bravo AF: 0.473

Asia WGS AF: 0.715 AC: 2448 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	19
DANN	Benign	0.85
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs997467; hg19: chr2-199182704;