rs4277680

Variant names:

• chr3-117887069-A-G
• rs4277680
• ENST00000484092.1:n.411+110113T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-117887069-A-G
• chr3-117887069-A-T

Variant summary

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

The ENST00000484092.1(LINC03051):​n.411+110113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,774 control chromosomes in the GnomAD database, including 11,544 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 0.39 (11544 hom., cov: 32)
• Consequence: LINC03051 ENST00000484092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798

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 (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03051	NR_182298.1	n.399-8263T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03051	ENST00000484092.1	n.411+110113T>C		intron_variant	Intron 1 of 1	4
LINC03051	ENST00000665851.1	n.399-8263T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58890 AN: 151656 Hom.: 11536 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 58938 AN: 151774 Hom.: 11544 Cov.: 32 AF XY: 0.390 AC XY: 28902 AN XY: 74172

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.388

Alfa AF: 0.383 Hom.: 2156

Bravo AF: 0.390

Asia WGS AF: 0.437 AC: 1516 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	5.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4277680; hg19: chr3-117605916;