rs4809918

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372666	XR_007067652.1	n.1666-414G>A		intron_variant	Intron 13 of 16
LOC105372666	XR_007067653.1	n.992-414G>A		intron_variant	Intron 8 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000421642.5	n.261-414G>A		intron_variant	Intron 3 of 4	5
LINC01524	ENST00000425279.6	n.402-414G>A		intron_variant	Intron 3 of 5	3
LINC01524	ENST00000437987.1	n.123+3111G>A		intron_variant	Intron 1 of 1	3

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 v4.3

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;