rs1426063

Variant names:

• chr4-75105711-A-G
• rs1426063
• ENST00000754017.1:n.332+16214T>C

Variant summary

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

The ENST00000754017.1(LINC02562):​n.332+16214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,086 control chromosomes in the GnomAD database, including 5,123 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 0.22 (5123 hom., cov: 32)
• Consequence: LINC02562 ENST00000754017.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 13 publications found

Genes affected

LINC02562 (HGNC:53602): (long intergenic non-protein coding RNA 2562)

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 = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754017.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02562	ENST00000754017.1		n.332+16214T>C		intron	N/A
	LINC02562	ENST00000754018.1		n.218+21355T>C		intron	N/A
	LINC02562	ENST00000754019.1		n.150-21008T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33426 AN: 151968 Hom.: 5116 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.220 AC: 33467 AN: 152086 Hom.: 5123 Cov.: 32 AF XY: 0.217 AC XY: 16109 AN XY: 74342

African (AFR) AF: 0.439 AC: 18179 AN: 41444

American (AMR) AF: 0.166 AC: 2541 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5186

South Asian (SAS) AF: 0.118 AC: 572 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10580

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9237 AN: 67984

Other (OTH) AF: 0.193 AC: 408 AN: 2116

Alfa AF: 0.166 Hom.: 5354

Bravo AF: 0.228

Asia WGS AF: 0.0990 AC: 346 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		-0.034

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1426063; hg19: chr4-76030921;