Variant chr3-53844589-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018397.5(CHDH):c.-131+1494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,760 control chromosomes in the GnomAD database, including 5,816 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 0.27 ( 5795 hom., cov: 33)

Exomes 𝑓: 0.26 ( 21 hom. )

Consequence

CHDH
NM_018397.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.938

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHDH	NM_018397.5 linkuse as main transcript	c.-131+1494G>A		intron_variant		ENST00000315251.11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
CHDH	ENST00000315251.11 linkuse as main transcript	c.-131+1494G>A	intron_variant		1	NM_018397.5	P1
CHDH	ENST00000481668.5 linkuse as main transcript	c.-138G>A	5_prime_UTR_variant	1/3	2
CHDH	ENST00000467802.1 linkuse as main transcript	c.-131+124G>A	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40750

AN:

152106

Hom.:

5789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.0662

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.269

GnomAD4 exome

AF:

0.256

AC:

136

AN:

532

Hom.:

Cov.:

AF XY:

0.237

AC XY:

AN XY:

400

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.0909

Gnomad4 SAS exome

AF:

0.200

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.367

GnomAD4 genome

AF:

0.268

AC:

40772

AN:

152228

Hom.:

5795

Cov.:

AF XY:

0.266

AC XY:

19783

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.0663

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.319

Gnomad4 NFE

AF:

0.315

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.305

Hom.:

11948

Bravo

AF:

0.262

Asia WGS

AF:

0.146

AC:

510

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.2

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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