20-52679623-T-C

Variant names:

• chr20-52679623-T-C
• rs1523537
• ENST00000413070.3:n.455-1782T>C

Variant summary

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

The ENST00000413070.3(LINC01524):​n.455-1782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,010 control chromosomes in the GnomAD database, including 13,771 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 0.42 (13771 hom., cov: 32)
• Consequence: LINC01524 ENST00000413070.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 16 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413070.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01524	ENST00000413070.3	TSL:3	n.455-1782T>C		intron	N/A
	LINC01524	ENST00000421642.5	TSL:5	n.260+2515T>C		intron	N/A
	LINC01524	ENST00000425279.6	TSL:3	n.256-1782T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64352 AN: 151892 Hom.: 13756 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64410 AN: 152010 Hom.: 13771 Cov.: 32 AF XY: 0.427 AC XY: 31704 AN XY: 74310

African (AFR) AF: 0.428 AC: 17719 AN: 41428

American (AMR) AF: 0.364 AC: 5564 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3472

East Asian (EAS) AF: 0.405 AC: 2091 AN: 5162

South Asian (SAS) AF: 0.612 AC: 2948 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4723 AN: 10574

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28567 AN: 67950

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.422 Hom.: 18430

Bravo AF: 0.411

Asia WGS AF: 0.523 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.85
DANN	Benign	0.57
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1523537; hg19: chr20-51296162;