rs10517302

Positions:

• chr4-34334448-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02484	ENST00000658479.1	n.423+481G>C		intron_variant

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;