3-55258959-T-C

Position:

• chr3-55258959-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183740.1(LINC02030):​n.483+12397T>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 NR_183740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

Genes affected

LINC02030 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.483+12397T>C		intron_variant
LINC02030	NR_183741.1	n.772+12397T>C		intron_variant
LINC02030	NR_183742.1	n.386+12397T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+25600T>C		intron_variant
LINC02030	ENST00000662390.1	n.320+25600T>C		intron_variant
LINC02030	ENST00000670191.1	n.212+12397T>C		intron_variant

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

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.496

Alfa AF: 0.489 Hom.: 9735

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6445726; hg19: chr3-55292987;