dbSNP rs861857: YDJC:c.*367G>C (chr22-21628051-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440

Publications

16 publications found

Variant links:

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]

YDJC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
YDJC	NM_001017964.2	MANE Select	c.*367G>C	downstream_gene	N/A	NP_001017964.1	A8MPS7-1
YDJC	NM_001371350.1		c.*711G>C	downstream_gene	N/A	NP_001358279.1	A8MPS7-2
YDJC	NR_163922.1		n.*38G>C	downstream_gene	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77773

AN:

151932

Hom.:

20618

Cov.:

show subpopulations

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.:

AF XY:

0.439

AC XY:

6834

AN XY:

15550

show subpopulations

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:

AN:

180

European-Non Finnish (NFE)

AF:

0.424

AC:

8954

AN:

21116

Other (OTH)

AF:

0.452

AC:

989

AN:

2190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

366

732

1097

1463

1829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.512

AC:

77886

AN:

152050

Hom.:

20669

Cov.:

AF XY:

0.516

AC XY:

38325

AN XY:

74322

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1915

3830

5746

7661

9576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.6

(source)

DANN

Benign

0.61

PhyloP100

-0.044

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over