rs16943468

Positions:

• chr17-59367748-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YPEL2	NM_001005404.4	c.117+14222T>C		intron_variant		ENST00000312655.9
YPEL2	XM_017024621.2	c.117+14222T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YPEL2	ENST00000312655.9	c.117+14222T>C		intron_variant		1	NM_001005404.4	P1
YPEL2	ENST00000585166.1	c.117+14222T>C		intron_variant		5		P1
YPEL2	ENST00000672916.2	c.216+14222T>C		intron_variant
YPEL2	ENST00000581865.1	n.137-20579T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.0691

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0628

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0912 Hom.: 184

Bravo AF: 0.122

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.63

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: rs16943468; hg19: chr17-57445109;