11-12050956-G-C

Variant names:

• chr11-12050956-G-C
• rs923175
• ENST00000531559.1:n.57-7578G>C

Variant summary

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

The ENST00000531559.1(LINC02547):​n.57-7578G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,128 control chromosomes in the GnomAD database, including 24,578 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 0.57 (24578 hom., cov: 33)
• Consequence: LINC02547 ENST00000531559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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.57-7578G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02547	ENST00000531559.1	TSL:2	n.57-7578G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86079 AN: 152010 Hom.: 24537 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.566 AC: 86165 AN: 152128 Hom.: 24578 Cov.: 33 AF XY: 0.563 AC XY: 41852 AN XY: 74374

African (AFR) AF: 0.597 AC: 24787 AN: 41494

American (AMR) AF: 0.474 AC: 7243 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2005 AN: 3472

East Asian (EAS) AF: 0.645 AC: 3325 AN: 5158

South Asian (SAS) AF: 0.579 AC: 2794 AN: 4824

European-Finnish (FIN) AF: 0.554 AC: 5870 AN: 10592

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38304 AN: 68004

Other (OTH) AF: 0.560 AC: 1179 AN: 2106

Alfa AF: 0.468 Hom.: 1414

Bravo AF: 0.563

Asia WGS AF: 0.594 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.58
PhyloP100		-0.95

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: rs923175;

hg19: chr11-12072503;