22-21627960-T-A

Variant names:

• chr22-21627960-T-A
• rs878825
• NM_001017964.2:c.*458A>T

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.*458A>T 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: 32)
  • 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: -1.43
• Publications: 38 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=-0.86).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YDJC	NM_001017964.2	MANE Select	c.*458A>T		downstream_gene	N/A	NP_001017964.1
	YDJC	NM_001371350.1		c.*802A>T		downstream_gene	N/A	NP_001358279.1
	YDJC	NR_163922.1		n.*129A>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YDJC	ENST00000292778.11	TSL:2 MANE Select	c.*458A>T		downstream_gene	N/A	ENSP00000292778.6
	YDJC	ENST00000398873.4	TSL:1	c.*802A>T		downstream_gene	N/A	ENSP00000381847.3
	YDJC	ENST00000415762.6	TSL:1	n.*1078A>T		downstream_gene	N/A	ENSP00000402481.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3404 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1696

African (AFR) AF: 0.00 AC: 0 AN: 130

American (AMR) AF: 0.00 AC: 0 AN: 82

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 148

East Asian (EAS) AF: 0.00 AC: 0 AN: 226

South Asian (SAS) AF: 0.00 AC: 0 AN: 64

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 102

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2430

Other (OTH) AF: 0.00 AC: 0 AN: 216

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6525

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.34
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs878825; hg19: chr22-21982249;