5-17912590-A-T

Variant names:

• chr5-17912590-A-T
• rs1443404
• ENST00000511596.5:n.196-7637A>T

Variant summary

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

The ENST00000511596.5(LINC02223):​n.196-7637A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,924 control chromosomes in the GnomAD database, including 15,703 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 0.45 (15703 hom., cov: 32)
• Consequence: LINC02223 ENST00000511596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 1 publications found

Genes affected

LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

ENSG00000294859 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02223	NR_134286.1	n.579-7637A>T		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-7637A>T		intron_variant	Intron 2 of 4	5
LINC02223	ENST00000514771.7	n.552-7637A>T		intron_variant	Intron 4 of 6	5
LINC02223	ENST00000650405.1	n.218-7637A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67815 AN: 151806 Hom.: 15695 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.447 AC: 67841 AN: 151924 Hom.: 15703 Cov.: 32 AF XY: 0.445 AC XY: 33037 AN XY: 74272

African (AFR) AF: 0.314 AC: 13033 AN: 41466

American (AMR) AF: 0.517 AC: 7864 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1982 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2534 AN: 5148

South Asian (SAS) AF: 0.512 AC: 2472 AN: 4826

European-Finnish (FIN) AF: 0.434 AC: 4586 AN: 10578

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33761 AN: 67902

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.471 Hom.: 2155

Bravo AF: 0.447

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.46
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1443404; hg19: chr5-17912699;