ENST00000503100.1:n.1918-2782C>T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC107986320 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02355	NR_125887.1	n.1918-2782C>T		intron_variant	Intron 9 of 12
LOC107986320	XR_001741885.1	n.433+1068G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02355	ENST00000503100.1	n.1918-2782C>T		intron_variant	Intron 9 of 12	1

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

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.437

Alfa AF: 0.454 Hom.: 2071

Bravo AF: 0.398

Asia WGS AF: 0.325 AC: 1131 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538317; hg19: chr4-150174374;