16-47785413-C-T

Variant names:

• chr16-47785413-C-T
• rs7202145
• ENST00000565451.5:n.280-29217C>T

Variant summary

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

The ENST00000565451.5(LINC02133):​n.280-29217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0852 in 152,256 control chromosomes in the GnomAD database, including 1,025 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 0.085 (1025 hom., cov: 32)
• Consequence: LINC02133 ENST00000565451.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 2 publications found

Genes affected

LINC02133 (HGNC:52993): (long intergenic non-protein coding RNA 2133)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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
LINC02133	ENST00000565451.5	n.280-29217C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12946 AN: 152136 Hom.: 1020 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0852 AC: 12972 AN: 152256 Hom.: 1025 Cov.: 32 AF XY: 0.0828 AC XY: 6162 AN XY: 74446

African (AFR) AF: 0.209 AC: 8685 AN: 41522

American (AMR) AF: 0.0500 AC: 765 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5188

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4822

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2809 AN: 68024

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0659 Hom.: 128

Bravo AF: 0.0937

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		0.098
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7202145; hg19: chr16-47819324;