rs4687889

Positions:

• chr3-117818592-T-C

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03051	ENST00000484092.1	n.412-146296A>G		intron_variant, non_coding_transcript_variant		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;