rs4687889

Variant names:

• chr3-117818592-T-C
• rs4687889
• ENST00000484092.1:n.412-146296A>G

Variant summary

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

The ENST00000484092.1(LINC03051):​n.412-146296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,950 control chromosomes in the GnomAD database, including 17,920 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 0.48 (17920 hom., cov: 32)
• Consequence: LINC03051 ENST00000484092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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.412-146296A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72429 AN: 151832 Hom.: 17923 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.477 AC: 72453 AN: 151950 Hom.: 17920 Cov.: 32 AF XY: 0.470 AC XY: 34934 AN XY: 74254

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0836

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.485

Alfa AF: 0.478 Hom.: 25008

Bravo AF: 0.489

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4687889; hg19: chr3-117537439;