rs16887451

Positions:

• chr5-17918466-A-C
• chr5-17918466-A-G
• chr5-17918466-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.579-1761A>C 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 0.106 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 NR_134286.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02223	NR_134286.1	n.579-1761A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-1761A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0932 Hom.: 688

Bravo AF: 0.106

Asia WGS AF: 0.0290 AC: 104 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16887451; hg19: chr5-17918575;