rs4811346

Variant names:

• chr20-52406570-A-C
• rs4811346
• ENST00000454600.1:n.335+51211A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-52406570-A-C
• chr20-52406570-A-G
• chr20-52406570-A-T

Variant summary

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

The ENST00000454600.1(LINC01524):​n.335+51211A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 148,432 control chromosomes in the GnomAD database, including 1,035 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 0.11 (1035 hom., cov: 31)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01524	ENST00000454600.1	TSL:3	n.335+51211A>C		intron	N/A
	LINC01524	ENST00000653220.2		n.461-45789A>C		intron	N/A
	LINC01524	ENST00000655073.2		n.368-35930A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 16943 AN: 148368 Hom.: 1030 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.114 AC: 16982 AN: 148432 Hom.: 1035 Cov.: 31 AF XY: 0.112 AC XY: 8090 AN XY: 72238

African (AFR) AF: 0.152 AC: 6168 AN: 40576

American (AMR) AF: 0.137 AC: 2048 AN: 14958

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3444

East Asian (EAS) AF: 0.101 AC: 516 AN: 5124

South Asian (SAS) AF: 0.0768 AC: 358 AN: 4660

European-Finnish (FIN) AF: 0.0734 AC: 681 AN: 9278

Middle Eastern (MID) AF: 0.124 AC: 36 AN: 290

European-Non Finnish (NFE) AF: 0.0961 AC: 6453 AN: 67124

Other (OTH) AF: 0.108 AC: 223 AN: 2068

Alfa AF: 0.0641 Hom.: 110

Bravo AF: 0.122

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs4811346; hg19: chr20-51023109;