chr22-21628051-C-G

Variant names:

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

Variant summary

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

The NM_001017964.2(YDJC):​c.*367G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 183,204 control chromosomes in the GnomAD database, including 23,891 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 0.51 (20669 hom., cov: 33)
  • Exomes 𝑓: 0.44 (3222 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YDJC	NM_001017964.2	c.*367G>C		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.*367G>C		downstream_gene_variant		2	NM_001017964.2	ENSP00000292778.6

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77773 AN: 151932 Hom.: 20618 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.444 AC: 13824 AN: 31154 Hom.: 3222 Cov.: 0 AF XY: 0.439 AC XY: 6834 AN XY: 15550

African (AFR) AF: 0.660 AC: 843 AN: 1278

American (AMR) AF: 0.557 AC: 476 AN: 854

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 548 AN: 1452

East Asian (EAS) AF: 0.452 AC: 1072 AN: 2370

South Asian (SAS) AF: 0.563 AC: 171 AN: 304

European-Finnish (FIN) AF: 0.489 AC: 690 AN: 1410

Middle Eastern (MID) AF: 0.450 AC: 81 AN: 180

European-Non Finnish (NFE) AF: 0.424 AC: 8954 AN: 21116

Other (OTH) AF: 0.452 AC: 989 AN: 2190

GnomAD4 genome AF: 0.512 AC: 77886 AN: 152050 Hom.: 20669 Cov.: 33 AF XY: 0.516 AC XY: 38325 AN XY: 74322

African (AFR) AF: 0.652 AC: 27048 AN: 41486

American (AMR) AF: 0.517 AC: 7903 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2708 AN: 5160

South Asian (SAS) AF: 0.528 AC: 2544 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5356 AN: 10586

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29471 AN: 67944

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.464 Hom.: 2404

Bravo AF: 0.520

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.6
DANN	Benign	0.61
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;