ENST00000654333.1:n.56-607A>C

Variant names:

• chr4-173734763-A-C
• rs4521323
• ENST00000654333.1:n.56-607A>C

Variant summary

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

The ENST00000654333.1(LINC02269):​n.56-607A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,714 control chromosomes in the GnomAD database, including 20,669 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 0.51 (20669 hom., cov: 30)
• Consequence: LINC02269 ENST00000654333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818
• Publications: 6 publications found

Genes affected

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

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 (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654333.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02269	ENST00000654333.1		n.56-607A>C		intron	N/A
	LINC02269	ENST00000654653.1		n.56-607A>C		intron	N/A
	LINC02269	ENST00000654916.1		n.56-607A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77433 AN: 151598 Hom.: 20658 Cov.: 30

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.511 AC: 77467 AN: 151714 Hom.: 20669 Cov.: 30 AF XY: 0.513 AC XY: 38053 AN XY: 74114

African (AFR) AF: 0.356 AC: 14698 AN: 41334

American (AMR) AF: 0.649 AC: 9878 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3909 AN: 5094

South Asian (SAS) AF: 0.554 AC: 2666 AN: 4808

European-Finnish (FIN) AF: 0.485 AC: 5105 AN: 10534

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37372 AN: 67956

Other (OTH) AF: 0.537 AC: 1129 AN: 2104

Alfa AF: 0.546 Hom.: 94901

Bravo AF: 0.517

Asia WGS AF: 0.641 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs4521323; hg19: chr4-174655914;