rs6047533

Variant names:

• chr20-21641440-G-A
• rs6047533
• ENST00000624692.1:n.265-13998C>T

Variant summary

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

The ENST00000624692.1(LINC01726):​n.265-13998C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,264 control chromosomes in the GnomAD database, including 702 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 0.070 (702 hom., cov: 32)
• Consequence: LINC01726 ENST00000624692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 2 publications found

Genes affected

LINC01726 (HGNC:52514): (long intergenic non-protein coding RNA 1726)

LINC01727 (HGNC:52515): (long intergenic non-protein coding RNA 1727)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624692.1. 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
	LINC01726	NR_109878.1		n.265-13998C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01726	ENST00000624692.1	TSL:1	n.265-13998C>T		intron	N/A
	LINC01727	ENST00000624367.4	TSL:5	n.802-10234G>A		intron	N/A
	LINC01727	ENST00000653224.1		n.660-24638G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10622 AN: 152146 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.00414

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0701 AC: 10669 AN: 152264 Hom.: 702 Cov.: 32 AF XY: 0.0683 AC XY: 5085 AN XY: 74462

African (AFR) AF: 0.170 AC: 7041 AN: 41526

American (AMR) AF: 0.0673 AC: 1030 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3468

East Asian (EAS) AF: 0.141 AC: 732 AN: 5174

South Asian (SAS) AF: 0.0478 AC: 231 AN: 4828

European-Finnish (FIN) AF: 0.00414 AC: 44 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1296 AN: 68034

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0383 Hom.: 1044

Bravo AF: 0.0823

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.1
DANN	Benign	0.70
PhyloP100		0.82

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: rs6047533;

hg19: chr20-21622078;