rs2403569

Variant names:

• chr11-12058704-C-A
• rs2403569
• ENST00000531559.1:n.227C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-12058704-C-A
• chr11-12058704-C-G

Variant summary

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

The ENST00000531559.1(LINC02547):​n.227C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,226 control chromosomes in the GnomAD database, including 24,412 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 0.56 (24403 hom., cov: 34)
  • Exomes 𝑓: 0.62 (9 hom.)
• Consequence: LINC02547 ENST00000531559.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 4 publications found

Genes affected

LINC02547 (HGNC:53582): (long intergenic non-protein coding RNA 2547)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531559.1. 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
	LINC02547	NR_135109.1		n.227C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02547	ENST00000531559.1	TSL:2	n.227C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85291 AN: 152066 Hom.: 24382 Cov.: 34

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.561

GnomAD4 exome AF: 0.619 AC: 26 AN: 42 Hom.: 9 Cov.: 0 AF XY: 0.588 AC XY: 20 AN XY: 34

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.647 AC: 22 AN: 34

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.561 AC: 85355 AN: 152184 Hom.: 24403 Cov.: 34 AF XY: 0.566 AC XY: 42108 AN XY: 74382

African (AFR) AF: 0.456 AC: 18919 AN: 41514

American (AMR) AF: 0.626 AC: 9578 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1674 AN: 3468

East Asian (EAS) AF: 0.611 AC: 3164 AN: 5182

South Asian (SAS) AF: 0.584 AC: 2816 AN: 4822

European-Finnish (FIN) AF: 0.720 AC: 7623 AN: 10584

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39814 AN: 67990

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.561 Hom.: 5244

Bravo AF: 0.552

Asia WGS AF: 0.562 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.85
PhyloP100		-0.15

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: rs2403569;

hg19: chr11-12080251;