rs8135758

chr22-21722116-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013313.5(YPEL1):c.-164-11208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,160 control chromosomes in the GnomAD database, including 1,692 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 0.13 (1692 hom., cov: 32)
• Consequence: YPEL1 NM_013313.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YPEL1	NM_013313.5	c.-164-11208C>T		intron_variant		ENST00000339468.8
YPEL1	XM_047441355.1	c.-165+1285C>T		intron_variant
YPEL1	NR_130910.2	n.181-11208C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YPEL1	ENST00000339468.8	c.-164-11208C>T		intron_variant		1	NM_013313.5	P1
YPEL1	ENST00000403503.1	c.-164-11208C>T		intron_variant		3
YPEL1	ENST00000477675.1	n.148-11208C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20254 AN: 152042 Hom.: 1692 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.133 AC: 20260 AN: 152160 Hom.: 1692 Cov.: 32 AF XY: 0.132 AC XY: 9816 AN XY: 74386

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.152

Alfa AF: 0.174 Hom.: 4902

Bravo AF: 0.127

Asia WGS AF: 0.0510 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	6.1
Dann	Benign	0.86

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: rs8135758; hg19: chr22-22076405;