22-21628573-C-A

Variant names:

• chr22-21628573-C-A
• rs1165498065
• NM_001017964.2:c.817G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001017964.2(YDJC):​c.817G>T​(p.Glu273*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: YDJC NM_001017964.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.10
• Publications: 0 publications found

Genes affected

YDJC (HGNC:27158): (YdjC chitooligosaccharide deacetylase homolog) Predicted to enable deacetylase activity and magnesium ion binding activity. Predicted to be involved in carbohydrate metabolic process. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017964.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YDJC	NM_001017964.2	MANE Select	c.817G>T	p.Glu273*	stop_gained	Exon 5 of 5	NP_001017964.1	A8MPS7-1
	YDJC	NM_001371350.1		c.*189G>T		3_prime_UTR	Exon 4 of 4	NP_001358279.1	A8MPS7-2
	YDJC	NR_163922.1		n.884G>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YDJC	ENST00000292778.11	TSL:2 MANE Select	c.817G>T	p.Glu273*	stop_gained	Exon 5 of 5	ENSP00000292778.6	A8MPS7-1
	YDJC	ENST00000398873.4	TSL:1	c.*189G>T		3_prime_UTR	Exon 4 of 4	ENSP00000381847.3	A8MPS7-2
	YDJC	ENST00000415762.6	TSL:1	n.*465G>T		non_coding_transcript_exon	Exon 5 of 5	ENSP00000402481.2	A8MPS7-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.49
CADD	Pathogenic	43
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.89
FATHMM_MKL	Pathogenic	0.98	D
PhyloP100		7.1
Vest4		0.17
GERP RS		4.3
Mutation Taster		=20/180	disease causing

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: rs1165498065; hg19: chr22-21982862;