chr5-17912590-A-T

Position:

• chr5-17912590-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134286.1(LINC02223):​n.579-7637A>T variant causes a intron, non coding transcript 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 NR_134286.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02223	NR_134286.1	n.579-7637A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-7637A>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.477

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443404; hg19: chr5-17912699;