3-55279372-A-G

Variant names:

• chr3-55279372-A-G
• rs358806
• ENST00000654581.1:n.363-6946A>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_183740.1(LINC02030):​n.484-6946A>G variant causes a 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: 34)
• Consequence: LINC02030 NR_183740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

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

LOC124906243 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.484-6946A>G		intron_variant	Intron 4 of 6
LINC02030	NR_183741.1	n.773-6946A>G		intron_variant	Intron 6 of 8
LINC02030	NR_183742.1	n.387-6946A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.363-6946A>G		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.321-6946A>G		intron_variant	Intron 3 of 5
LINC02030	ENST00000670191.1	n.213-6946A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs358806; hg19: chr3-55313400;