chr14-86005780-C-T

Position:

• chr14-86005780-C-T

Variant summary

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

The NR_110155.1(LINC02328):​n.185-65083C>T 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 0.0247 in 151,924 control chromosomes in the GnomAD database, including 156 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 0.025 (156 hom., cov: 32)
• Consequence: LINC02328 NR_110155.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02328	NR_110155.1	n.185-65083C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02328	ENST00000668344.3	n.254-65083C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3727 AN: 151806 Hom.: 155 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0247 AC: 3755 AN: 151924 Hom.: 156 Cov.: 32 AF XY: 0.0276 AC XY: 2049 AN XY: 74232

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0205

Alfa AF: 0.0174 Hom.: 135

Bravo AF: 0.0284

Asia WGS AF: 0.0970 AC: 335 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.042
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7492316; hg19: chr14-86472124;