rs10520852

Variant names:

• chr5-17892328-T-A
• rs10520852
• ENST00000511596.5:n.196-27899T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-17892328-T-A
• chr5-17892328-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000511596.5(LINC02223):​n.196-27899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 152,268 control chromosomes in the GnomAD database, including 21 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 0.013 (21 hom., cov: 32)
• Consequence: LINC02223 ENST00000511596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• 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=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0128 (1956/152268) while in subpopulation SAS AF = 0.0482 (232/4816). AF 95% confidence interval is 0.0431. There are 21 homozygotes in GnomAd4. There are 955 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02223	NR_134286.1	n.578+19242T>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-27899T>A		intron_variant	Intron 2 of 4	5
LINC02223	ENST00000514771.7	n.551+19242T>A		intron_variant	Intron 4 of 6	5
LINC02223	ENST00000650405.1	n.218-27899T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0128 AC: 1955 AN: 152150 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00355

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0128 AC: 1956 AN: 152268 Hom.: 21 Cov.: 32 AF XY: 0.0128 AC XY: 955 AN XY: 74470

African (AFR) AF: 0.00354 AC: 147 AN: 41566

American (AMR) AF: 0.00556 AC: 85 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0482 AC: 232 AN: 4816

European-Finnish (FIN) AF: 0.0123 AC: 131 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1228 AN: 68016

Other (OTH) AF: 0.0166 AC: 35 AN: 2112

Alfa AF: 0.00346 Hom.: 2

Bravo AF: 0.0111

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.78
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10520852; hg19: chr5-17892437;