3-117873501-C-A

Position:

• chr3-117873501-C-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03051	ENST00000484092.1	n.411+123681G>T		intron_variant, non_coding_transcript_variant		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;