rs12146602

Variant names:

• chr11-13833179-G-A
• rs12146602
• ENST00000530492.1:n.79-5899C>T

Variant summary

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

The ENST00000530492.1(LINC02545):​n.79-5899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,116 control chromosomes in the GnomAD database, including 1,597 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 0.12 (1597 hom., cov: 32)
• Consequence: LINC02545 ENST00000530492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 2 publications found

Genes affected

LINC02545 (HGNC:53580): (long intergenic non-protein coding RNA 2545)

LINC02548 (HGNC:53583): (long intergenic non-protein coding RNA 2548)

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 (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530492.1. 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
	LINC02548	NR_149108.1		n.201-14528G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02545	ENST00000530492.1	TSL:3	n.79-5899C>T		intron	N/A
	LINC02548	ENST00000531749.1	TSL:3	n.189-14528G>A		intron	N/A
	LINC02548	ENST00000648524.1		n.587-7476G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18922 AN: 152000 Hom.: 1594 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.125 AC: 18945 AN: 152116 Hom.: 1597 Cov.: 32 AF XY: 0.121 AC XY: 8989 AN XY: 74372

African (AFR) AF: 0.232 AC: 9609 AN: 41450

American (AMR) AF: 0.116 AC: 1768 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3466

East Asian (EAS) AF: 0.107 AC: 552 AN: 5180

South Asian (SAS) AF: 0.117 AC: 565 AN: 4822

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5171 AN: 68004

Other (OTH) AF: 0.124 AC: 262 AN: 2108

Alfa AF: 0.0971 Hom.: 2775

Bravo AF: 0.137

Asia WGS AF: 0.128 AC: 446 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	1.8
DANN	Benign	0.59
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12146602; hg19: chr11-13854726;