rs12936897

chr17-59347284-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YPEL2	NM_001005404.4	c.-195-5931G>A		intron_variant		ENST00000312655.9
YPEL2	XM_017024621.2	c.-195-5931G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YPEL2	ENST00000312655.9	c.-195-5931G>A		intron_variant		1	NM_001005404.4	P1
YPEL2	ENST00000585166.1	c.-196+1989G>A		intron_variant		5		P1
YPEL2	ENST00000581865.1	n.136+15460G>A		intron_variant, non_coding_transcript_variant		2
YPEL2	ENST00000582192.1	n.105-5931G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.418

Alfa AF: 0.400 Hom.: 16155

Bravo AF: 0.429

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.71
Dann	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs12936897; hg19: chr17-57424645;