rs12659663

Variant names:

• chr5-17877308-T-C
• rs12659663
• ENST00000511596.5:n.196-42919T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-17877308-T-C
• chr5-17877308-T-G

Variant summary

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

The ENST00000511596.5(LINC02223):​n.196-42919T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,966 control chromosomes in the GnomAD database, including 32,154 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 0.61 (32154 hom., cov: 32)
• Consequence: LINC02223 ENST00000511596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02223	NR_134286.1	n.578+4222T>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-42919T>C		intron_variant	Intron 2 of 4	5
LINC02223	ENST00000514771.7	n.551+4222T>C		intron_variant	Intron 4 of 6	5
LINC02223	ENST00000650405.1	n.218-42919T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93197 AN: 151846 Hom.: 32144 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.613 AC: 93227 AN: 151966 Hom.: 32154 Cov.: 32 AF XY: 0.614 AC XY: 45599 AN XY: 74274

African (AFR) AF: 0.267 AC: 11078 AN: 41432

American (AMR) AF: 0.767 AC: 11702 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2768 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3490 AN: 5154

South Asian (SAS) AF: 0.717 AC: 3456 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7109 AN: 10562

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.756 AC: 51361 AN: 67956

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.706 Hom.: 93637

Bravo AF: 0.605

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.72
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12659663; hg19: chr5-17877417;