2-30152320-C-T

Position:

• chr2-30152320-C-T

Variant summary

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

The NM_016061.3(YPEL5):​c.-24-4308C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,040 control chromosomes in the GnomAD database, including 5,752 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 0.26 (5752 hom., cov: 33)
• Consequence: YPEL5 NM_016061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

YPEL5 (HGNC:18329): (yippee like 5) Predicted to enable metal ion binding activity. Predicted to be involved in cell population proliferation. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YPEL5	NM_016061.3	c.-24-4308C>T		intron_variant		ENST00000261353.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YPEL5	ENST00000261353.9	c.-24-4308C>T		intron_variant		1	NM_016061.3	P1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39326 AN: 151922 Hom.: 5738 Cov.: 33

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.259 AC: 39364 AN: 152040 Hom.: 5752 Cov.: 33 AF XY: 0.262 AC XY: 19460 AN XY: 74288

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.246

Alfa AF: 0.215 Hom.: 4982

Bravo AF: 0.271

Asia WGS AF: 0.467 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1345151; hg19: chr2-30375186;