5-17918466-A-C

Variant names:

• chr5-17918466-A-C
• rs16887451
• ENST00000511596.5:n.196-1761A>C

Variant summary

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

The ENST00000511596.5(LINC02223):​n.196-1761A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,210 control chromosomes in the GnomAD database, including 935 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 0.11 (935 hom., cov: 33)
• Consequence: LINC02223 ENST00000511596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511596.5. 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
	LINC02223	NR_134286.1		n.579-1761A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02223	ENST00000511596.5	TSL:5	n.196-1761A>C		intron	N/A
	LINC02223	ENST00000514771.7	TSL:5	n.552-1761A>C		intron	N/A
	LINC02223	ENST00000650405.1		n.218-1761A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16092 AN: 152092 Hom.: 936 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.106 AC: 16094 AN: 152210 Hom.: 935 Cov.: 33 AF XY: 0.105 AC XY: 7789 AN XY: 74426

African (AFR) AF: 0.142 AC: 5916 AN: 41520

American (AMR) AF: 0.0769 AC: 1175 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5182

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1204 AN: 10602

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6776 AN: 68010

Other (OTH) AF: 0.104 AC: 219 AN: 2112

Alfa AF: 0.0955 Hom.: 1055

Bravo AF: 0.106

Asia WGS AF: 0.0290 AC: 104 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.72
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs16887451; hg19: chr5-17918575;