Genetic Variant YDJC:p.Ala263Thr (chr22-21628603-C-T) – 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.787G>A(p.Ala263Thr) variant causes a missense change. The variant allele was found at a frequency of 0.203 in 1,601,686 control chromosomes in the GnomAD database, including 37,640 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 0.18 ( 3355 hom., cov: 33)

Exomes 𝑓: 0.21 ( 34285 hom. )

Consequence

YDJC
NM_001017964.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.10

Publications

123 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 (MetaRNN=0.0015680492).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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	HGVSp	Effect	Exon Rank	Protein	UniProt
YDJC	NM_001017964.2	MANE Select	c.787G>A	p.Ala263Thr	missense	Exon 5 of 5	NP_001017964.1	A8MPS7-1
YDJC	NM_001371350.1		c.*159G>A		3_prime_UTR	Exon 4 of 4	NP_001358279.1	A8MPS7-2
YDJC	NR_163922.1		n.854G>A		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
YDJC	ENST00000292778.11	TSL:2 MANE Select	c.787G>A	p.Ala263Thr	missense	Exon 5 of 5	ENSP00000292778.6	A8MPS7-1
YDJC	ENST00000398873.4	TSL:1	c.*159G>A		3_prime_UTR	Exon 4 of 4	ENSP00000381847.3	A8MPS7-2
YDJC	ENST00000415762.6	TSL:1	n.*435G>A		non_coding_transcript_exon	Exon 5 of 5	ENSP00000402481.2	A8MPS7-3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27528

AN:

152052

Hom.:

3349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0524

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.407

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.194

GnomAD2 exomes

AF:

0.266

AC:

60275

AN:

226654

AF XY:

0.260

show subpopulations

Gnomad AFR exome

AF:

0.0504

Gnomad AMR exome

AF:

0.470

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.415

Gnomad FIN exome

AF:

0.308

Gnomad NFE exome

AF:

0.196

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.205

AC:

297244

AN:

1449516

Hom.:

34285

Cov.:

AF XY:

0.206

AC XY:

148585

AN XY:

720136

show subpopulations

African (AFR)

AF:

0.0450

AC:

1496

AN:

33280

American (AMR)

AF:

0.451

AC:

19377

AN:

42990

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

6159

AN:

25930

East Asian (EAS)

AF:

0.384

AC:

15051

AN:

39176

South Asian (SAS)

AF:

0.273

AC:

23391

AN:

85550

European-Finnish (FIN)

AF:

0.299

AC:

15241

AN:

50928

Middle Eastern (MID)

AF:

0.236

AC:

1350

AN:

5720

European-Non Finnish (NFE)

AF:

0.183

AC:

202748

AN:

1106144

Other (OTH)

AF:

0.208

AC:

12431

AN:

59798

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

15182

30364

45546

60728

75910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7342

14684

22026

29368

36710

<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:

0.181

AC:

27528

AN:

152170

Hom.:

3355

Cov.:

AF XY:

0.192

AC XY:

14242

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0522

AC:

2172

AN:

41570

American (AMR)

AF:

0.303

AC:

4634

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

818

AN:

3470

East Asian (EAS)

AF:

0.407

AC:

2100

AN:

5156

South Asian (SAS)

AF:

0.266

AC:

1283

AN:

4832

European-Finnish (FIN)

AF:

0.314

AC:

3314

AN:

10564

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.186

AC:

12615

AN:

67974

Other (OTH)

AF:

0.193

AC:

409

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1123

2245

3368

4490

5613

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<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:

0.197

Hom.:

10954

Bravo

AF:

0.180

TwinsUK

AF:

0.183

AC:

678

ALSPAC

AF:

0.165

AC:

636

ESP6500AA

AF:

0.0498

AC:

218

ESP6500EA

AF:

0.185

AC:

1582

ExAC

AF:

0.239

AC:

28541

Asia WGS

AF:

0.316

AC:

1099

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0026

Eigen

Uncertain

0.26

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.91

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.4

PhyloP100

7.1

PrimateAI

Uncertain

0.64

PROVEAN

Benign

-0.40

REVEL

Benign

0.11

Sift

Benign

0.16

Sift4G

Benign

0.34

Polyphen

0.88

Vest4

0.054

MPC

0.87

ClinPred

0.022

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.13

gMVP

0.46

Mutation Taster

=88/12

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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