chr3-55279372-A-C

Variant names:

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

Variant summary

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

The ENST00000654581.1(LINC02030):​n.363-6946A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,216 control chromosomes in the GnomAD database, including 52,099 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 0.82 (52099 hom., cov: 34)
• Consequence: LINC02030 ENST00000654581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 28 publications found

Genes affected

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

ENSG00000242775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.484-6946A>C		intron_variant	Intron 4 of 6
LINC02030	NR_183741.1	n.773-6946A>C		intron_variant	Intron 6 of 8
LINC02030	NR_183742.1	n.387-6946A>C		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>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.321-6946A>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000670191.1	n.213-6946A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125446 AN: 152098 Hom.: 52051 Cov.: 34

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.825 AC: 125550 AN: 152216 Hom.: 52099 Cov.: 34 AF XY: 0.824 AC XY: 61290 AN XY: 74404

African (AFR) AF: 0.889 AC: 36941 AN: 41548

American (AMR) AF: 0.810 AC: 12405 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2736 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4082 AN: 5178

South Asian (SAS) AF: 0.912 AC: 4398 AN: 4822

European-Finnish (FIN) AF: 0.744 AC: 7866 AN: 10572

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54446 AN: 68008

Other (OTH) AF: 0.806 AC: 1702 AN: 2112

Alfa AF: 0.808 Hom.: 177344

Bravo AF: 0.828

Asia WGS AF: 0.863 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.43
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs358806; hg19: chr3-55313400;