rs10498284

Variant names:

• chr14-25819095-G-A
• rs10498284
• ENST00000546412.2:n.537+16755C>T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.537+16755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,960 control chromosomes in the GnomAD database, including 4,285 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 0.19 (4285 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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
LINC02306	ENST00000546412.2	n.537+16755C>T		intron_variant	Intron 5 of 9	3
LINC02306	ENST00000657312.1	n.702+16790C>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28262 AN: 151842 Hom.: 4265 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.186 AC: 28332 AN: 151960 Hom.: 4285 Cov.: 32 AF XY: 0.187 AC XY: 13854 AN XY: 74274

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.0766

Gnomad4 OTH AF: 0.163

Alfa AF: 0.144 Hom.: 641

Bravo AF: 0.201

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498284; hg19: chr14-26288301;