rs12425791

Variant names:

• chr12-674318-G-A
• rs12425791
• NR_187480.1:n.1174C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-674318-G-A
• chr12-674318-G-C

Variant summary

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

The NR_187480.1(LINC02455):​n.1174C>T 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 0.187 in 152,100 control chromosomes in the GnomAD database, including 2,957 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 0.19 (2957 hom., cov: 32)
• Consequence: LINC02455 NR_187480.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 86 publications found

Genes affected

LINC02455 (HGNC:53388): (long intergenic non-protein coding RNA 2455)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02455	NR_187480.1	n.1174C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28417 AN: 151982 Hom.: 2954 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.187 AC: 28428 AN: 152100 Hom.: 2957 Cov.: 32 AF XY: 0.192 AC XY: 14250 AN XY: 74352

African (AFR) AF: 0.112 AC: 4630 AN: 41510

American (AMR) AF: 0.256 AC: 3900 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1347 AN: 5166

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4814

European-Finnish (FIN) AF: 0.184 AC: 1948 AN: 10584

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13363 AN: 67980

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.198 Hom.: 13675

Bravo AF: 0.187

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.74
DANN	Benign	0.76
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12425791; hg19: chr12-783484;