ENST00000619758.1:n.99+3G>A

Variant names:

• chr15-74379184-G-A
• rs4555110
• ENST00000619758.2:n.141+3G>A

Variant summary

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

The ENST00000619758.2(LINC02255):​n.141+3G>A variant causes a splice region, intron 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 ENST00000619758.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 5 publications found

Genes affected

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

ENSG00000302041 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619758.2. 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
	LINC02255	NR_146881.1		n.100+3G>A		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02255	ENST00000619758.2	TSL:5	n.141+3G>A		splice_region intron	N/A
	ENSG00000302041	ENST00000783573.1		n.116-9106C>T		intron	N/A
	ENSG00000302041	ENST00000783574.1		n.102-3754C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 2 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.208 AC: 5 AN: 24

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.292 AC: 12112 AN: 41478

American (AMR) AF: 0.165 AC: 2528 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1631 AN: 5158

South Asian (SAS) AF: 0.323 AC: 1556 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10604

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.139 AC: 9481 AN: 68000

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.165 Hom.: 1174

Bravo AF: 0.202

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.90
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs4555110; hg19: chr15-74671525;