rs4811340

Variant names:

• chr20-52393218-G-C
• rs4811340
• ENST00000454600.1:n.335+37859G>C

Variant summary

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

The ENST00000454600.1(LINC01524):​n.335+37859G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,982 control chromosomes in the GnomAD database, including 16,668 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 0.44 (16668 hom., cov: 32)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 10 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454600.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01524	ENST00000454600.1	TSL:3	n.335+37859G>C		intron	N/A
	LINC01524	ENST00000653220.2		n.460+52566G>C		intron	N/A
	LINC01524	ENST00000655073.2		n.368-49282G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67413 AN: 151864 Hom.: 16615 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.444 AC: 67532 AN: 151982 Hom.: 16668 Cov.: 32 AF XY: 0.437 AC XY: 32427 AN XY: 74272

African (AFR) AF: 0.675 AC: 27985 AN: 41482

American (AMR) AF: 0.391 AC: 5973 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5162

South Asian (SAS) AF: 0.368 AC: 1769 AN: 4812

European-Finnish (FIN) AF: 0.277 AC: 2917 AN: 10538

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24482 AN: 67940

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.403 Hom.: 1669

Bravo AF: 0.461

Asia WGS AF: 0.415 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.38
DANN	Benign	0.73
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4811340; hg19: chr20-51009757;