rs5754727

Variant names:

• chr22-21702984-G-A
• rs5754727
• NM_013313.5:c.270+386C>T

Variant summary

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

The NM_013313.5(YPEL1):​c.270+386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,042 control chromosomes in the GnomAD database, including 20,160 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 0.51 (20160 hom., cov: 32)
• Consequence: YPEL1 NM_013313.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 10 publications found

Genes affected

YPEL1 (HGNC:12845): (yippee like 1) This gene is located in the region associated with DiGeorge syndrome on chromosome 22. The encoded protein localizes to the centrosome and nucleolus and may play a role in the regulation of cell division. [provided by RefSeq, Feb 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YPEL1	NM_013313.5	c.270+386C>T		intron_variant	Intron 4 of 4	ENST00000339468.8	NP_037445.1
YPEL1	NR_130910.2	n.998+386C>T		intron_variant	Intron 4 of 4
YPEL1	XM_047441355.1	c.270+386C>T		intron_variant	Intron 4 of 4		XP_047297311.1
YPEL1	XM_047441356.1	c.270+386C>T		intron_variant	Intron 4 of 4		XP_047297312.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YPEL1	ENST00000339468.8	c.270+386C>T		intron_variant	Intron 4 of 4	1	NM_013313.5	ENSP00000342832.3
YPEL1	ENST00000672036.2	c.375+386C>T		intron_variant	Intron 3 of 3			ENSP00000500196.2
YPEL1	ENST00000477675.1	n.965+386C>T		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76785 AN: 151922 Hom.: 20137 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.505 AC: 76853 AN: 152042 Hom.: 20160 Cov.: 32 AF XY: 0.511 AC XY: 38006 AN XY: 74314

African (AFR) AF: 0.612 AC: 25369 AN: 41482

American (AMR) AF: 0.498 AC: 7612 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1901 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3756 AN: 5154

South Asian (SAS) AF: 0.500 AC: 2414 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5697 AN: 10576

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.420 AC: 28544 AN: 67948

Other (OTH) AF: 0.503 AC: 1060 AN: 2106

Alfa AF: 0.451 Hom.: 13853

Bravo AF: 0.509

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-1.5
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: rs5754727; hg19: chr22-22057273;