rs12874142

Variant names:

• chr13-42403673-C-T
• rs12874142
• ENST00000637462.1:n.712-8223C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.712-8223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,088 control chromosomes in the GnomAD database, including 2,439 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 0.16 (2439 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 7 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

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 (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. 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
	LINC02341	ENST00000637462.1	TSL:5	n.712-8223C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24370 AN: 151970 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.160 AC: 24376 AN: 152088 Hom.: 2439 Cov.: 32 AF XY: 0.158 AC XY: 11751 AN XY: 74340

African (AFR) AF: 0.0496 AC: 2059 AN: 41504

American (AMR) AF: 0.142 AC: 2177 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3466

East Asian (EAS) AF: 0.136 AC: 703 AN: 5182

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1696 AN: 10554

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14731 AN: 67968

Other (OTH) AF: 0.175 AC: 368 AN: 2104

Alfa AF: 0.178 Hom.: 927

Bravo AF: 0.152

Asia WGS AF: 0.236 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12874142; hg19: chr13-42977809;