ENST00000658479.1:n.423+481G>C

Variant names:

• chr4-34334448-C-G
• rs10517302
• ENST00000658479.1:n.423+481G>C

Variant summary

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

The ENST00000658479.1(LINC02484):​n.423+481G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,180 control chromosomes in the GnomAD database, including 3,132 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 0.17 (3132 hom., cov: 32)
• Consequence: LINC02484 ENST00000658479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

LINC02484 (HGNC:53459): (long intergenic non-protein coding RNA 2484)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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
LINC02484	ENST00000658479.1	n.423+481G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26480 AN: 152062 Hom.: 3113 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.174 AC: 26544 AN: 152180 Hom.: 3132 Cov.: 32 AF XY: 0.175 AC XY: 13058 AN XY: 74418

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.173

Alfa AF: 0.140 Hom.: 247

Bravo AF: 0.187

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517302; hg19: chr4-34336070;