Variant rs2298428 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YDJC	NM_001017964.2 linkuse as main transcript	c.787G>A	p.Ala263Thr	missense_variant	5/5	ENST00000292778.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YDJC	ENST00000292778.11 linkuse as main transcript	c.787G>A	p.Ala263Thr	missense_variant	5/5	2	NM_001017964.2	P1	A8MPS7-1

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

GnomAD3 exomes

AF:

0.266

AC:

60275

AN:

226654

Hom.:

9689

AF XY:

0.260

AC XY:

32336

AN XY:

124588

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 SAS exome

AF:

0.277

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

Gnomad4 AFR exome

AF:

0.0450

Gnomad4 AMR exome

AF:

0.451

Gnomad4 ASJ exome

AF:

0.238

Gnomad4 EAS exome

AF:

0.384

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.299

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.181

AC:

27528

AN:

152170

Hom.:

3355

Cov.:

AF XY:

0.192

AC XY:

14242

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0522

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.196

Hom.:

5699

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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.56

CADD

Benign

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

MutationTaster

Benign

0.022

P;P

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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over