14-97157256-G-A

Variant names:

• chr14-97157256-G-A
• rs12432865
• ENST00000554445.2:n.322-1349G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554445.2(LINC02304):​n.322-1349G>A variant causes a intron 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 ENST00000554445.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554445.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02304	NR_146554.1		n.314-1349G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02304	ENST00000554445.2	TSL:3	n.322-1349G>A		intron	N/A
	LINC02304	ENST00000717121.1		n.536+2087G>A		intron	N/A
	LINC02304	ENST00000717122.1		n.293+2087G>A		intron	N/A

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

African (AFR) AF: 0.0881 AC: 3657 AN: 41532

American (AMR) AF: 0.290 AC: 4428 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2071 AN: 5178

South Asian (SAS) AF: 0.165 AC: 793 AN: 4818

European-Finnish (FIN) AF: 0.188 AC: 1985 AN: 10584

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9262 AN: 67994

Other (OTH) AF: 0.177 AC: 375 AN: 2114

Alfa AF: 0.147 Hom.: 8659

Bravo AF: 0.161

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.59
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs12432865; hg19: chr14-97623593;