rs10520010

Variant names:

• chr4-149204230-C-T
• rs10520010
• ENST00000503100.1:n.1053+78C>T

Variant summary

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

The ENST00000503100.1(LINC02355):​n.1053+78C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,890 control chromosomes in the GnomAD database, including 2,718 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 0.19 (2718 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02355 ENST00000503100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 3 publications found

Genes affected

LINC02355 (HGNC:53277): (long intergenic non-protein coding RNA 2355)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02355	NR_125887.1	n.1053+78C>T		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02355	ENST00000503100.1	n.1053+78C>T		intron_variant	Intron 4 of 12	1
LINC02355	ENST00000827371.1	n.291+78C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28321 AN: 151772 Hom.: 2724 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.187 AC: 28331 AN: 151890 Hom.: 2718 Cov.: 33 AF XY: 0.191 AC XY: 14150 AN XY: 74236

African (AFR) AF: 0.182 AC: 7569 AN: 41496

American (AMR) AF: 0.161 AC: 2448 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1120 AN: 5130

South Asian (SAS) AF: 0.320 AC: 1546 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2373 AN: 10572

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11945 AN: 67870

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.185 Hom.: 354

Bravo AF: 0.181

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.19
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10520010; hg19: chr4-150125382;