rs381062

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-55233363-A-C
• chr3-55233363-A-G
• chr3-55233363-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_183741.1(LINC02030):​n.369+4A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LINC02030 NR_183741.1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183741.1. 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
	LINC02030	NR_183740.1		n.352+2506A>C		intron	N/A
	LINC02030	NR_183741.1		n.369+4A>C		splice_region intron	N/A
	LINC02030	NR_183742.1		n.114+6395A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02030	ENST00000654581.1		n.362+4A>C		splice_region intron	N/A
	LINC02030	ENST00000662390.1		n.320+4A>C		splice_region intron	N/A
	LINC02030	ENST00000809726.1		n.284+43749A>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.54
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;