20-52666556-C-T

Variant names:

• chr20-52666556-C-T
• rs707544
• ENST00000656362.1:n.722-2592C>T

Variant summary

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

The ENST00000656362.1(LINC01524):​n.722-2592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,212 control chromosomes in the GnomAD database, including 62,961 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 0.91 (62961 hom., cov: 31)
• Consequence: LINC01524 ENST00000656362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656362.1. 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	ENST00000656362.1		n.722-2592C>T		intron	N/A
	LINC01524	ENST00000666751.1		n.642-163C>T		intron	N/A
	LINC01524	ENST00000716895.1		n.357-163C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138058 AN: 152094 Hom.: 62897 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.908 AC: 138182 AN: 152212 Hom.: 62961 Cov.: 31 AF XY: 0.906 AC XY: 67393 AN XY: 74412

African (AFR) AF: 0.975 AC: 40495 AN: 41548

American (AMR) AF: 0.872 AC: 13331 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3235 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3816 AN: 5170

South Asian (SAS) AF: 0.921 AC: 4443 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9335 AN: 10582

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60427 AN: 68008

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.895 Hom.: 120988

Bravo AF: 0.907

Asia WGS AF: 0.863 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.31
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs707544;

hg19: chr20-51283095;