rs13041126

chr20-52476457-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666751.1(LINC01524):n.174-54431T>C variant causes a intron, non coding transcript 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 ENST00000666751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

Genes affected

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

LOC105372666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.463-54431T>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.426-54431T>C		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754671.2	n.426-54431T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01524	ENST00000666751.1	n.174-54431T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.261

Alfa AF: 0.261 Hom.: 909

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13041126; hg19: chr20-51092996;