3-55258959-T-C

Variant names:

• chr3-55258959-T-C
• rs6445726
• ENST00000654581.1:n.362+25600T>C

Variant summary

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

The ENST00000654581.1(LINC02030):​n.362+25600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,898 control chromosomes in the GnomAD database, including 18,805 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 (18805 hom., cov: 32)
• Consequence: LINC02030 ENST00000654581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.483+12397T>C		intron_variant	Intron 4 of 6
LINC02030	NR_183741.1	n.772+12397T>C		intron_variant	Intron 6 of 8
LINC02030	NR_183742.1	n.386+12397T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+25600T>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000662390.1	n.320+25600T>C		intron_variant	Intron 3 of 5
LINC02030	ENST00000670191.1	n.212+12397T>C		intron_variant	Intron 2 of 4
LINC02030	ENST00000809726.1	n.285-27359T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75407 AN: 151780 Hom.: 18786 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.497 AC: 75473 AN: 151898 Hom.: 18805 Cov.: 32 AF XY: 0.501 AC XY: 37168 AN XY: 74210

African (AFR) AF: 0.460 AC: 19039 AN: 41428

American (AMR) AF: 0.535 AC: 8159 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2469 AN: 5118

South Asian (SAS) AF: 0.367 AC: 1766 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6364 AN: 10572

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34150 AN: 67932

Other (OTH) AF: 0.496 AC: 1045 AN: 2108

Alfa AF: 0.491 Hom.: 10840

Bravo AF: 0.495

Asia WGS AF: 0.438 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.42
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6445726; hg19: chr3-55292987;