14-28984835-A-G

Position:

• chr14-28984835-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_184205.1(LINC02326):​n.338-5817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,162 control chromosomes in the GnomAD database, including 2,268 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 (2268 hom., cov: 32)
• Consequence: LINC02326 NR_184205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

ENSG00000258028 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02326	NR_184205.1	n.338-5817T>C		intron_variant
LINC02326	NR_184206.1	n.237-5817T>C		intron_variant
LOC107984685	XR_007064101.1	n.202-1565A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258028	ENST00000551227.1	n.108-1565A>G		intron_variant		5
LINC02326	ENST00000552028.2	n.462-5817T>C		intron_variant		3
LINC02326	ENST00000650159.1	n.292+44605T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22628 AN: 152042 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.149 AC: 22638 AN: 152162 Hom.: 2268 Cov.: 32 AF XY: 0.155 AC XY: 11500 AN XY: 74382

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.159

Alfa AF: 0.148 Hom.: 298

Bravo AF: 0.145

Asia WGS AF: 0.342 AC: 1182 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12587874; hg19: chr14-29454041;