chr2-30152320-C-T

Variant names:

• chr2-30152320-C-T
• rs1345151
• NM_016061.3:c.-24-4308C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016061.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL5	NM_016061.3	MANE Select	c.-24-4308C>T		intron	N/A	NP_057145.1	P62699
	YPEL5	NM_001127399.2		c.-25+4015C>T		intron	N/A	NP_001120871.1	P62699
	YPEL5	NM_001127400.2		c.-25+3779C>T		intron	N/A	NP_001120872.1	P62699

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL5	ENST00000261353.9	TSL:1 MANE Select	c.-24-4308C>T		intron	N/A	ENSP00000261353.4	P62699
	YPEL5	ENST00000402708.5	TSL:1	c.-85-3530C>T		intron	N/A	ENSP00000385278.1	P62699
	YPEL5	ENST00000379519.7	TSL:2	c.-25+3779C>T		intron	N/A	ENSP00000368834.3	P62699

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

African (AFR) AF: 0.341 AC: 14118 AN: 41434

American (AMR) AF: 0.256 AC: 3908 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2964 AN: 5180

South Asian (SAS) AF: 0.370 AC: 1788 AN: 4826

European-Finnish (FIN) AF: 0.152 AC: 1607 AN: 10548

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13585 AN: 67990

Other (OTH) AF: 0.246 AC: 521 AN: 2114

Alfa AF: 0.218 Hom.: 6436

Bravo AF: 0.271

Asia WGS AF: 0.467 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.72
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1345151; hg19: chr2-30375186;