dbSNP rs4563403: CHDH:c.*990G>A (chr3-53816787-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_018397.5(CHDH):c.*990G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 150,556 control chromosomes in the GnomAD database, including 4,828 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 0.22 ( 4828 hom., cov: 30)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

CHDH
NM_018397.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.201

Publications

14 publications found

Variant links:

Genes affected

CHDH (HGNC:24288): (choline dehydrogenase) The protein encoded by this gene is a choline dehydrogenase that localizes to the mitochondrion. Variations in this gene can affect susceptibility to choline deficiency. A few transcript variants have been found for this gene, but the full-length nature of only one has been characterized to date. [provided by RefSeq, Dec 2010]

CHDH 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018397.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHDH	NM_018397.5	MANE Select	c.*990G>A		3_prime_UTR	Exon 9 of 9	NP_060867.2	Q8NE62

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHDH	ENST00000315251.11	TSL:1 MANE Select	c.*990G>A	3_prime_UTR	Exon 9 of 9	ENSP00000319851.5	Q8NE62
CHDH	ENST00000875879.1		c.*990G>A	3_prime_UTR	Exon 9 of 9	ENSP00000545938.1
CHDH	ENST00000875892.1		c.*990G>A	3_prime_UTR	Exon 9 of 9	ENSP00000545951.1

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32447

AN:

150444

Hom.:

4813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.160

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.198

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0714

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.216

AC:

32506

AN:

150540

Hom.:

4828

Cov.:

AF XY:

0.216

AC XY:

15854

AN XY:

73424

show subpopulations

African (AFR)

AF:

0.417

AC:

16981

AN:

40706

American (AMR)

AF:

0.238

AC:

3605

AN:

15140

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

552

AN:

3468

East Asian (EAS)

AF:

0.168

AC:

860

AN:

5116

South Asian (SAS)

AF:

0.118

AC:

561

AN:

4766

European-Finnish (FIN)

AF:

0.134

AC:

1370

AN:

10194

Middle Eastern (MID)

AF:

0.156

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.119

AC:

8093

AN:

67866

Other (OTH)

AF:

0.198

AC:

413

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1141

2281

3422

4562

5703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.153

Hom.:

1675

Bravo

AF:

0.236

Asia WGS

AF:

0.169

AC:

590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

6.0

(source)

DANN

Benign

0.57

PhyloP100

0.20

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over