20-52684661-G-A

Variant names:

• chr20-52684661-G-A
• rs4809918
• ENST00000421642.5:n.261-414G>A

Variant summary

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

The ENST00000421642.5(LINC01524):​n.261-414G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,194 control chromosomes in the GnomAD database, including 232 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 0.044 (232 hom., cov: 32)
• Consequence: LINC01524 ENST00000421642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421642.5. 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	ENST00000421642.5	TSL:5	n.261-414G>A		intron	N/A
	LINC01524	ENST00000425279.6	TSL:3	n.402-414G>A		intron	N/A
	LINC01524	ENST00000437987.1	TSL:3	n.123+3111G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0434 AC: 6598 AN: 152076 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0436 AC: 6636 AN: 152194 Hom.: 232 Cov.: 32 AF XY: 0.0459 AC XY: 3413 AN XY: 74408

African (AFR) AF: 0.0345 AC: 1433 AN: 41548

American (AMR) AF: 0.106 AC: 1621 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3464

East Asian (EAS) AF: 0.133 AC: 684 AN: 5142

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4826

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0311 AC: 2118 AN: 67998

Other (OTH) AF: 0.0398 AC: 84 AN: 2112

Alfa AF: 0.0365 Hom.: 590

Bravo AF: 0.0503

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.54
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4809918; hg19: chr20-51301200;