17-59367748-T-C

Variant names:

• chr17-59367748-T-C
• rs16943468
• NM_001005404.4:c.117+14222T>C

Variant summary

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

The NM_001005404.4(YPEL2):​c.117+14222T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,180 control chromosomes in the GnomAD database, including 1,581 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 0.12 (1581 hom., cov: 32)
• Consequence: YPEL2 NM_001005404.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

YPEL2 (HGNC:18326): (yippee like 2) Predicted to enable metal ion binding activity. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

YPEL2 Gene-Disease associations (from GenCC):

• retinitis pigmentosa

  Inheritance: AD Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005404.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL2	NM_001005404.4	MANE Select	c.117+14222T>C		intron	N/A	NP_001005404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YPEL2	ENST00000312655.9	TSL:1 MANE Select	c.117+14222T>C		intron	N/A	ENSP00000312272.4
	YPEL2	ENST00000672916.2		c.216+14222T>C		intron	N/A	ENSP00000500006.2
	YPEL2	ENST00000585166.1	TSL:5	c.117+14222T>C		intron	N/A	ENSP00000464285.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17979 AN: 152062 Hom.: 1573 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.118 AC: 18019 AN: 152180 Hom.: 1581 Cov.: 32 AF XY: 0.118 AC XY: 8754 AN XY: 74418

African (AFR) AF: 0.236 AC: 9794 AN: 41488

American (AMR) AF: 0.0573 AC: 876 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0691 AC: 240 AN: 3472

East Asian (EAS) AF: 0.193 AC: 996 AN: 5164

South Asian (SAS) AF: 0.155 AC: 747 AN: 4824

European-Finnish (FIN) AF: 0.0628 AC: 666 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4354 AN: 68008

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.0947 Hom.: 203

Bravo AF: 0.122

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		-1.1
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: rs16943468; hg19: chr17-57445109;