rs861857

Positions:

• chr22-21628051-C-G
• chr22-21628051-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 22-21628051-C-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
YDJC	NM_001017964.2			downstream_gene_variant		ENST00000292778.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YDJC	ENST00000292778.11			downstream_gene_variant		2	NM_001017964.2	P1
YDJC	ENST00000415762.6			downstream_gene_variant		1
YDJC	ENST00000464015.5			downstream_gene_variant		1
YDJC	ENST00000468686.5			downstream_gene_variant		1

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

Gnomad4 AFR exome AF: 0.660

Gnomad4 AMR exome AF: 0.557

Gnomad4 ASJ exome AF: 0.377

Gnomad4 EAS exome AF: 0.452

Gnomad4 SAS exome AF: 0.563

Gnomad4 FIN exome AF: 0.489

Gnomad4 NFE exome AF: 0.424

Gnomad4 OTH exome AF: 0.452

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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.506

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs861857; hg19: chr22-21982340;