rs13041126

Variant names:

• chr20-52476457-T-C
• rs13041126
• ENST00000454600.1:n.336-54431T>C

Variant summary

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

The ENST00000454600.1(LINC01524):​n.336-54431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,992 control chromosomes in the GnomAD database, including 5,202 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 0.26 (5202 hom., cov: 31)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 23 publications found

Genes affected

LINC01524 (HGNC:51228): (long intergenic non-protein coding RNA 1524)

LOC105372666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) 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
LOC105372666	XR_001754670.2	n.426-54431T>C		intron_variant	Intron 3 of 11
LOC105372666	XR_001754671.2	n.426-54431T>C		intron_variant	Intron 3 of 6
LOC105372666	XR_007067652.1	n.463-54431T>C		intron_variant	Intron 4 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000454600.1	n.336-54431T>C		intron_variant	Intron 4 of 6	3
LINC01524	ENST00000655073.2	n.506+33819T>C		intron_variant	Intron 2 of 4
LINC01524	ENST00000656362.1	n.253+33819T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38848 AN: 151874 Hom.: 5201 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.256 AC: 38855 AN: 151992 Hom.: 5202 Cov.: 31 AF XY: 0.257 AC XY: 19063 AN XY: 74288

African (AFR) AF: 0.193 AC: 8006 AN: 41464

American (AMR) AF: 0.315 AC: 4814 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5160

South Asian (SAS) AF: 0.290 AC: 1393 AN: 4804

European-Finnish (FIN) AF: 0.217 AC: 2290 AN: 10560

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19097 AN: 67964

Other (OTH) AF: 0.261 AC: 549 AN: 2104

Alfa AF: 0.269 Hom.: 9348

Bravo AF: 0.260

Asia WGS AF: 0.287 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.51
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs13041126; hg19: chr20-51092996;