rs6022029

Variant names:

• chr20-52658626-A-G
• rs6022029
• ENST00000656362.1:n.722-10522A>G

Variant summary

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

The ENST00000656362.1(LINC01524):​n.722-10522A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,146 control chromosomes in the GnomAD database, including 1,211 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 0.090 (1211 hom., cov: 32)
• Consequence: LINC01524 ENST00000656362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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.722-10522A>G		intron	N/A
	LINC01524	ENST00000666751.1		n.642-8093A>G		intron	N/A
	LINC01524	ENST00000716895.1		n.357-8093A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13693 AN: 152028 Hom.: 1191 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0905 AC: 13764 AN: 152146 Hom.: 1211 Cov.: 32 AF XY: 0.0896 AC XY: 6665 AN XY: 74382

African (AFR) AF: 0.228 AC: 9455 AN: 41448

American (AMR) AF: 0.100 AC: 1532 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 65 AN: 3466

East Asian (EAS) AF: 0.137 AC: 709 AN: 5160

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4828

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0210 AC: 1430 AN: 68014

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0446 Hom.: 215

Bravo AF: 0.103

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.16

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: rs6022029;

hg19: chr20-51275165;