rs379850

Variant names:

• chr3-55248807-C-A
• rs379850
• ENST00000654581.1:n.362+15448C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-55248807-C-A
• chr3-55248807-C-T

Variant summary

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

The ENST00000654581.1(LINC02030):​n.362+15448C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,906 control chromosomes in the GnomAD database, including 18,785 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 0.50 (18785 hom., cov: 31)
• Consequence: LINC02030 ENST00000654581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.483+2245C>A		intron_variant	Intron 4 of 6
LINC02030	NR_183741.1	n.772+2245C>A		intron_variant	Intron 6 of 8
LINC02030	NR_183742.1	n.386+2245C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+15448C>A		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.320+15448C>A		intron_variant	Intron 3 of 5
LINC02030	ENST00000670191.1	n.212+2245C>A		intron_variant	Intron 2 of 4
LINC02030	ENST00000809726.1	n.285-37511C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75159 AN: 151786 Hom.: 18781 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.495 AC: 75196 AN: 151906 Hom.: 18785 Cov.: 31 AF XY: 0.491 AC XY: 36418 AN XY: 74236

African (AFR) AF: 0.533 AC: 22052 AN: 41410

American (AMR) AF: 0.462 AC: 7051 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3466

East Asian (EAS) AF: 0.508 AC: 2602 AN: 5122

South Asian (SAS) AF: 0.617 AC: 2960 AN: 4794

European-Finnish (FIN) AF: 0.388 AC: 4103 AN: 10564

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33232 AN: 67968

Other (OTH) AF: 0.491 AC: 1039 AN: 2116

Alfa AF: 0.356 Hom.: 904

Bravo AF: 0.498

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs379850; hg19: chr3-55282835;