chr17-14947369-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC02096	ENST00000754170.1	n.635-448G>T		intron_variant	Intron 3 of 4
LINC02096	ENST00000754171.1	n.910-448G>T		intron_variant	Intron 4 of 6

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

African (AFR) AF: 0.724 AC: 30023 AN: 41486

American (AMR) AF: 0.319 AC: 4880 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1607 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4816

European-Finnish (FIN) AF: 0.433 AC: 4565 AN: 10552

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25887 AN: 67972

Other (OTH) AF: 0.445 AC: 940 AN: 2112

Alfa AF: 0.378 Hom.: 5905

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10521290; hg19: chr17-14850686;