19-12897793-G-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000159.4(GCDH):c.1173G>T(p.Gly391Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,612,912 control chromosomes in the GnomAD database, including 103,534 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7709 hom., cov: 30)

Exomes 𝑓: 0.36 ( 95825 hom. )

Consequence

GCDH
NM_000159.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -1.11

Publications

27 publications found

Variant links:

Genes affected

GCDH (HGNC:4189): (glutaryl-CoA dehydrogenase) The protein encoded by this gene belongs to the acyl-CoA dehydrogenase family. It catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO(2) in the degradative pathway of L-lysine, L-hydroxylysine, and L-tryptophan metabolism. It uses electron transfer flavoprotein as its electron acceptor. The enzyme exists in the mitochondrial matrix as a homotetramer of 45-kD subunits. Mutations in this gene result in the metabolic disorder glutaric aciduria type 1, which is also known as glutaric acidemia type I. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 12. [provided by RefSeq, Mar 2013]

GCDH Gene-Disease associations (from GenCC):

glutaryl-CoA dehydrogenase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet, G2P, Myriad Women’s Health

GCDH links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 19-12897793-G-T is Benign according to our data. Variant chr19-12897793-G-T is described in ClinVar as Benign. ClinVar VariationId is 92529.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.11 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
GCDH	NM_000159.4 link	c.1173G>T	p.Gly391Gly	synonymous_variant	Exon 11 of 12	ENST00000222214.10	NP_000150.1
GCDH	NM_013976.5 link	c.1173G>T	p.Gly391Gly	synonymous_variant	Exon 11 of 12		NP_039663.1
GCDH	NR_102316.1 link	n.1336G>T		non_coding_transcript_exon_variant	Exon 11 of 12
GCDH	NR_102317.1 link	n.1554G>T		non_coding_transcript_exon_variant	Exon 10 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCDH	ENST00000222214.10 link	c.1173G>T	p.Gly391Gly	synonymous_variant	Exon 11 of 12	1	NM_000159.4	ENSP00000222214.4		Q92947-1

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46581

AN:

151716

Hom.:

7691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.317

GnomAD2 exomes

AF:

0.330

AC:

83034

AN:

251404

AF XY:

0.328

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.447

Gnomad ASJ exome

AF:

0.286

Gnomad EAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.301

Gnomad NFE exome

AF:

0.370

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.355

AC:

519119

AN:

1461078

Hom.:

95825

Cov.:

AF XY:

0.352

AC XY:

255790

AN XY:

726844

show subpopulations

African (AFR)

AF:

0.189

AC:

6330

AN:

33462

American (AMR)

AF:

0.441

AC:

19740

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

7399

AN:

26134

East Asian (EAS)

AF:

0.130

AC:

5173

AN:

39696

South Asian (SAS)

AF:

0.272

AC:

23422

AN:

86248

European-Finnish (FIN)

AF:

0.307

AC:

16372

AN:

53388

Middle Eastern (MID)

AF:

0.298

AC:

1719

AN:

5766

European-Non Finnish (NFE)

AF:

0.377

AC:

418806

AN:

1111292

Other (OTH)

AF:

0.334

AC:

20158

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

19103

38206

57309

76412

95515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13050

26100

39150

52200

65250

<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:

0.307

AC:

46632

AN:

151834

Hom.:

7709

Cov.:

AF XY:

0.303

AC XY:

22507

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.202

AC:

8352

AN:

41424

American (AMR)

AF:

0.391

AC:

5959

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

986

AN:

3468

East Asian (EAS)

AF:

0.145

AC:

750

AN:

5156

South Asian (SAS)

AF:

0.264

AC:

1269

AN:

4800

European-Finnish (FIN)

AF:

0.296

AC:

3130

AN:

10576

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.369

AC:

25077

AN:

67884

Other (OTH)

AF:

0.322

AC:

677

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1533

3066

4600

6133

7666

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.350

Hom.:

14819

Bravo

AF:

0.313

Asia WGS

AF:

0.250

AC:

870

AN:

3478

EpiCase

AF:

0.369

EpiControl

AF:

0.368

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Glutaric aciduria, type 1

Benign:4

Nov 19, 2019

Natera, Inc.

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Jun 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not specified

Benign:3

Aug 13, 2018

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 16, 2016

Mayo Clinic Laboratories, Mayo Clinic

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Elevated circulating glutaric acid concentration

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.77

(source)

DANN

Benign

0.89

PhyloP100

-1.1

PromoterAI

-0.045

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over