rs1158811

Variant names:

• chr6-68323676-A-G
• rs1158811
• ENST00000445346.1:n.237+3269T>C

Variant summary

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

The ENST00000445346.1(LINC02549):​n.237+3269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,966 control chromosomes in the GnomAD database, including 5,797 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 0.27 (5797 hom., cov: 32)
• Consequence: LINC02549 ENST00000445346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 3 publications found

Genes affected

LINC02549 (HGNC:53584): (long intergenic non-protein coding RNA 2549)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445346.1. 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
	LINC02549	NR_125854.1		n.237+3269T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02549	ENST00000445346.1	TSL:1	n.237+3269T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40678 AN: 151848 Hom.: 5786 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.268 AC: 40704 AN: 151966 Hom.: 5797 Cov.: 32 AF XY: 0.267 AC XY: 19834 AN XY: 74278

African (AFR) AF: 0.353 AC: 14617 AN: 41420

American (AMR) AF: 0.205 AC: 3126 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.0689 AC: 356 AN: 5166

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4818

European-Finnish (FIN) AF: 0.252 AC: 2661 AN: 10576

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17333 AN: 67954

Other (OTH) AF: 0.226 AC: 475 AN: 2106

Alfa AF: 0.268 Hom.: 1005

Bravo AF: 0.263

Asia WGS AF: 0.159 AC: 551 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.41
PhyloP100		0.063

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: rs1158811;

hg19: chr6-69033568;