rs12432865

Positions:

• chr14-97157256-G-A

Variant summary

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

The NR_146554.1(LINC02304):​n.314-1349G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,182 control chromosomes in the GnomAD database, including 2,319 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 0.15 (2319 hom., cov: 32)
• Consequence: LINC02304 NR_146554.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

LINC02304 (HGNC:53223): (long intergenic non-protein coding RNA 2304)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02304	NR_146554.1	n.314-1349G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02304	ENST00000554445.1	n.314-1349G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23081 AN: 152064 Hom.: 2320 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.152 AC: 23073 AN: 152182 Hom.: 2319 Cov.: 32 AF XY: 0.156 AC XY: 11627 AN XY: 74386

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.177

Alfa AF: 0.143 Hom.: 3665

Bravo AF: 0.161

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12432865; hg19: chr14-97623593;