22-21627960-T-C

Variant names:

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

Variant summary

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

The NM_001017964.2(YDJC):​c.*458A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 155,396 control chromosomes in the GnomAD database, including 9,265 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 0.32 (9171 hom., cov: 32)
  • Exomes 𝑓: 0.20 (94 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YDJC	NM_001017964.2	c.*458A>G		downstream_gene_variant		ENST00000292778.11	NP_001017964.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YDJC	ENST00000292778.11	c.*458A>G		downstream_gene_variant		2	NM_001017964.2	ENSP00000292778.6

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48671 AN: 151886 Hom.: 9127 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.202 AC: 684 AN: 3392 Hom.: 94 AF XY: 0.208 AC XY: 351 AN XY: 1686

African (AFR) AF: 0.362 AC: 47 AN: 130

American (AMR) AF: 0.293 AC: 24 AN: 82

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 29 AN: 148

East Asian (EAS) AF: 0.299 AC: 67 AN: 224

South Asian (SAS) AF: 0.406 AC: 26 AN: 64

European-Finnish (FIN) AF: 0.250 AC: 25 AN: 100

Middle Eastern (MID) AF: 0.667 AC: 4 AN: 6

European-Non Finnish (NFE) AF: 0.171 AC: 414 AN: 2424

Other (OTH) AF: 0.224 AC: 48 AN: 214

GnomAD4 genome AF: 0.321 AC: 48769 AN: 152004 Hom.: 9171 Cov.: 32 AF XY: 0.332 AC XY: 24646 AN XY: 74284

African (AFR) AF: 0.481 AC: 19935 AN: 41456

American (AMR) AF: 0.364 AC: 5555 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3464

East Asian (EAS) AF: 0.515 AC: 2663 AN: 5172

South Asian (SAS) AF: 0.394 AC: 1899 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3660 AN: 10548

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13380 AN: 67952

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.239 Hom.: 6525

Bravo AF: 0.331

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.51
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;