NM_001005404.4:c.-195-5931G>A

Variant names:

• chr17-59347284-G-A
• rs12936897
• NM_001005404.4:c.-195-5931G>A

Variant summary

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

The NM_001005404.4(YPEL2):​c.-195-5931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,970 control chromosomes in the GnomAD database, including 14,036 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 0.42 (14036 hom., cov: 31)
• Consequence: YPEL2 NM_001005404.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.55 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.-195-5931G>A		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.-195-5931G>A		intron	N/A	ENSP00000312272.4
	YPEL2	ENST00000585166.1	TSL:5	c.-196+1989G>A		intron	N/A	ENSP00000464285.1
	YPEL2	ENST00000581865.1	TSL:2	n.136+15460G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64510 AN: 151852 Hom.: 14021 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.425 AC: 64560 AN: 151970 Hom.: 14036 Cov.: 31 AF XY: 0.426 AC XY: 31634 AN XY: 74270

African (AFR) AF: 0.467 AC: 19348 AN: 41448

American (AMR) AF: 0.433 AC: 6609 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2197 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2733 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4345 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26771 AN: 67964

Other (OTH) AF: 0.418 AC: 882 AN: 2108

Alfa AF: 0.401 Hom.: 19389

Bravo AF: 0.429

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.63
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs12936897; hg19: chr17-57424645;