rs10498284

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546412.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02306	ENST00000546412.2	TSL:3	n.537+16755C>T		intron	N/A
	LINC02306	ENST00000657312.2		n.959+16790C>T		intron	N/A
	LINC02306	ENST00000736904.1		n.279+16755C>T		intron	N/A

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

African (AFR) AF: 0.419 AC: 17333 AN: 41400

American (AMR) AF: 0.152 AC: 2318 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.178 AC: 920 AN: 5164

South Asian (SAS) AF: 0.199 AC: 959 AN: 4818

European-Finnish (FIN) AF: 0.0813 AC: 860 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5202 AN: 67944

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.131 Hom.: 3587

Bravo AF: 0.201

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.32
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10498284; hg19: chr14-26288301;