rs538317

Variant names:

• chr4-149253222-C-T
• rs538317
• ENST00000503100.1:n.1918-2782C>T

Variant summary

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

The ENST00000503100.1(LINC02355):​n.1918-2782C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,562 control chromosomes in the GnomAD database, including 13,908 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 0.41 (13908 hom., cov: 32)
• Consequence: LINC02355 ENST00000503100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02355	NR_125887.1		n.1918-2782C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02355	ENST00000503100.1	TSL:1	n.1918-2782C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62628 AN: 151444 Hom.: 13898 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.413 AC: 62659 AN: 151562 Hom.: 13908 Cov.: 32 AF XY: 0.405 AC XY: 29991 AN XY: 74010

African (AFR) AF: 0.252 AC: 10415 AN: 41378

American (AMR) AF: 0.380 AC: 5774 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1542 AN: 3458

East Asian (EAS) AF: 0.332 AC: 1699 AN: 5110

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4814

European-Finnish (FIN) AF: 0.502 AC: 5275 AN: 10506

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34906 AN: 67788

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.445 Hom.: 2099

Bravo AF: 0.398

Asia WGS AF: 0.325 AC: 1131 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs538317; hg19: chr4-150174374;