22-21628051-C-T

Variant names:

• chr22-21628051-C-T
• rs861857
• NM_001017964.2:c.*367G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001017964.2(YDJC):​c.*367G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: YDJC NM_001017964.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 16 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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.*367G>A		downstream_gene	N/A	NP_001017964.1	A8MPS7-1
	YDJC	NM_001371350.1		c.*711G>A		downstream_gene	N/A	NP_001358279.1	A8MPS7-2
	YDJC	NR_163922.1		n.*38G>A		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YDJC	ENST00000292778.11	TSL:2 MANE Select	c.*367G>A		downstream_gene	N/A	ENSP00000292778.6	A8MPS7-1
	YDJC	ENST00000398873.4	TSL:1	c.*711G>A		downstream_gene	N/A	ENSP00000381847.3	A8MPS7-2
	YDJC	ENST00000415762.6	TSL:1	n.*987G>A		downstream_gene	N/A	ENSP00000402481.2	A8MPS7-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 31278 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 15612

African (AFR) AF: 0.00 AC: 0 AN: 1280

American (AMR) AF: 0.00 AC: 0 AN: 856

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1456

East Asian (EAS) AF: 0.00 AC: 0 AN: 2384

South Asian (SAS) AF: 0.00 AC: 0 AN: 304

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1414

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 182

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 21200

Other (OTH) AF: 0.00 AC: 0 AN: 2202

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.95
PhyloP100		-0.044

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs861857; hg19: chr22-21982340;