Genetic Variant NM_001017964.2:c.*367G>C (chr22-21628051-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 (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 link	c.*367G>C		downstream_gene_variant		ENST00000292778.11	NP_001017964.1	A8MPS7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YDJC	ENST00000292778.11 link	c.*367G>C		downstream_gene_variant		2	NM_001017964.2	ENSP00000292778.6		A8MPS7-1

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

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.:

AF XY:

0.516

AC XY:

38325

AN XY:

74322

show subpopulations

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

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