rs4555110

chr15-74379184-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146881.1(LINC02255):n.100+3G>A variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,178 control chromosomes in the GnomAD database, including 3,326 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 0.20 (3325 hom., cov: 31)
  • Exomes 𝑓: 0.20 (1 hom.)
• Consequence: LINC02255 NR_146881.1 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

Genes affected

LINC02255 (HGNC:53153): (long intergenic non-protein coding RNA 2255)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02255	NR_146881.1	n.100+3G>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02255	ENST00000619758.1	n.99+3G>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29735 AN: 152014 Hom.: 3308 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.196 AC: 9 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.235 AC XY: 8 AN XY: 34

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.196 AC: 29800 AN: 152132 Hom.: 3325 Cov.: 31 AF XY: 0.196 AC XY: 14561 AN XY: 74374

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.183

Alfa AF: 0.165 Hom.: 1035

Bravo AF: 0.202

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.6
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4555110; hg19: chr15-74671525;