17-14947369-G-T

Variant names:

• chr17-14947369-G-T
• rs10521290
• ENST00000664152.1:n.910-448G>T

Variant summary

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

The ENST00000664152.1(LINC02096):​n.910-448G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,062 control chromosomes in the GnomAD database, including 18,732 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 0.47 (18732 hom., cov: 33)
• Consequence: LINC02096 ENST00000664152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

Genes affected

LINC02096 (HGNC:52947): (long intergenic non-protein coding RNA 2096)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02096	ENST00000664152.1	n.910-448G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71166 AN: 151944 Hom.: 18692 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.469 AC: 71250 AN: 152062 Hom.: 18732 Cov.: 33 AF XY: 0.465 AC XY: 34518 AN XY: 74312

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.445

Alfa AF: 0.373 Hom.: 5130

Bravo AF: 0.472

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521290; hg19: chr17-14850686;