chr3-117873501-C-A

Variant names:

• chr3-117873501-C-A
• rs6804394
• ENST00000484092.1:n.411+123681G>T

Variant summary

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

The ENST00000484092.1(LINC03051):​n.411+123681G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,926 control chromosomes in the GnomAD database, including 18,226 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 0.49 (18226 hom., cov: 31)
• Consequence: LINC03051 ENST00000484092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

LINC03051 (HGNC:56330): (long intergenic non-protein coding RNA 3051)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03051	ENST00000484092.1	n.411+123681G>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73848 AN: 151808 Hom.: 18202 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.487 AC: 73924 AN: 151926 Hom.: 18226 Cov.: 31 AF XY: 0.490 AC XY: 36383 AN XY: 74258

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.472

Alfa AF: 0.453 Hom.: 3670

Bravo AF: 0.475

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6804394; hg19: chr3-117592348;