3-55233363-A-G

Variant names:

• chr3-55233363-A-G
• rs381062
• ENST00000654581.1:n.362+4A>G

Variant summary

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

The ENST00000654581.1(LINC02030):​n.362+4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,128 control chromosomes in the GnomAD database, including 55,897 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 0.85 (55897 hom., cov: 31)
• Consequence: LINC02030 ENST00000654581.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 6 publications found

Genes affected

LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)

LOC124906243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.352+2506A>G		intron_variant	Intron 3 of 6
LINC02030	NR_183741.1	n.369+4A>G		splice_region_variant, intron_variant	Intron 3 of 8
LINC02030	NR_183742.1	n.114+6395A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+4A>G		splice_region_variant, intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.320+4A>G		splice_region_variant, intron_variant	Intron 3 of 5
LINC02030	ENST00000809726.1	n.284+43749A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129874 AN: 152010 Hom.: 55867 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.854 AC: 129962 AN: 152128 Hom.: 55897 Cov.: 31 AF XY: 0.860 AC XY: 63987 AN XY: 74376

African (AFR) AF: 0.751 AC: 31174 AN: 41484

American (AMR) AF: 0.913 AC: 13971 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5145 AN: 5150

South Asian (SAS) AF: 0.971 AC: 4683 AN: 4822

European-Finnish (FIN) AF: 0.888 AC: 9404 AN: 10588

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59392 AN: 68000

Other (OTH) AF: 0.868 AC: 1832 AN: 2110

Alfa AF: 0.867 Hom.: 159836

Bravo AF: 0.849

Asia WGS AF: 0.962 AC: 3347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.3
DANN	Benign	0.59
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs381062; hg19: chr3-55267391;