ENST00000503100.1:n.1918-5905C>T

Variant names:

• chr4-149250099-C-T
• rs10520011
• ENST00000503100.1:n.1918-5905C>T

Variant summary

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

The ENST00000503100.1(LINC02355):​n.1918-5905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0471 in 151,880 control chromosomes in the GnomAD database, including 374 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 0.047 (374 hom., cov: 32)
• Consequence: LINC02355 ENST00000503100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 0 publications found

Genes affected

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

LOC107986320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503100.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02355	NR_125887.1		n.1918-5905C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02355	ENST00000503100.1	TSL:1	n.1918-5905C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7123 AN: 151762 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0471 AC: 7156 AN: 151880 Hom.: 374 Cov.: 32 AF XY: 0.0456 AC XY: 3386 AN XY: 74234

African (AFR) AF: 0.132 AC: 5468 AN: 41428

American (AMR) AF: 0.0270 AC: 411 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3466

East Asian (EAS) AF: 0.0224 AC: 115 AN: 5128

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4820

European-Finnish (FIN) AF: 0.00990 AC: 105 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 793 AN: 67892

Other (OTH) AF: 0.0452 AC: 95 AN: 2100

Alfa AF: 0.0274 Hom.: 47

Bravo AF: 0.0512

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10520011;

hg19: chr4-150171251;