rs10517302

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC02484	ENST00000758394.1	n.420+481G>C		intron_variant	Intron 1 of 5
LINC02484	ENST00000758397.1	n.414+481G>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.312 AC: 12953 AN: 41492

American (AMR) AF: 0.201 AC: 3076 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1405 AN: 5178

South Asian (SAS) AF: 0.166 AC: 803 AN: 4824

European-Finnish (FIN) AF: 0.0875 AC: 927 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6434 AN: 68020

Other (OTH) AF: 0.173 AC: 365 AN: 2114

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10517302; hg19: chr4-34336070;