rs12992463

Variant names:

• chr2-22328233-A-C
• rs12992463
• ENST00000450551.1:n.71-117239T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-22328233-A-C
• chr2-22328233-A-G

Variant summary

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

The ENST00000450551.1(LINC01830):​n.71-117239T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,102 control chromosomes in the GnomAD database, including 11,767 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 0.37 (11767 hom., cov: 32)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 6 publications found

Genes affected

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450551.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01830	ENST00000450551.1	TSL:5	n.71-117239T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56243 AN: 151984 Hom.: 11771 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.370 AC: 56238 AN: 152102 Hom.: 11767 Cov.: 32 AF XY: 0.363 AC XY: 27010 AN XY: 74344

African (AFR) AF: 0.203 AC: 8428 AN: 41498

American (AMR) AF: 0.314 AC: 4800 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1532 AN: 3468

East Asian (EAS) AF: 0.114 AC: 591 AN: 5174

South Asian (SAS) AF: 0.388 AC: 1872 AN: 4826

European-Finnish (FIN) AF: 0.415 AC: 4389 AN: 10568

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

European-Non Finnish (NFE) AF: 0.491 AC: 33340 AN: 67964

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.457 Hom.: 47410

Bravo AF: 0.355

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.61
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12992463;

hg19: chr2-22551105;