3-53815483-A-G

Variant names:

• chr3-53815483-A-G
• rs4687587
• NM_018397.5:c.*2294T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018397.5(CHDH):​c.*2294T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,244 control chromosomes in the GnomAD database, including 47,043 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 0.78 (47036 hom., cov: 33)
  • Exomes 𝑓: 0.73 (7 hom.)
• Consequence: CHDH NM_018397.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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.*2294T>C		3_prime_UTR	Exon 9 of 9	NP_060867.2	Q8NE62

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHDH	ENST00000315251.11	TSL:1 MANE Select	c.*2294T>C		3_prime_UTR	Exon 9 of 9	ENSP00000319851.5	Q8NE62

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118395 AN: 152100 Hom.: 46970 Cov.: 33

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.780

GnomAD4 exome AF: 0.731 AC: 19 AN: 26 Hom.: 7 Cov.: 0 AF XY: 0.682 AC XY: 15 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.778 AC: 14 AN: 18

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.779 AC: 118521 AN: 152218 Hom.: 47036 Cov.: 33 AF XY: 0.781 AC XY: 58115 AN XY: 74414

African (AFR) AF: 0.919 AC: 38177 AN: 41554

American (AMR) AF: 0.803 AC: 12289 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5174 AN: 5186

South Asian (SAS) AF: 0.821 AC: 3965 AN: 4828

European-Finnish (FIN) AF: 0.673 AC: 7125 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47017 AN: 67984

Other (OTH) AF: 0.783 AC: 1650 AN: 2108

Alfa AF: 0.748 Hom.: 17465

Bravo AF: 0.794

Asia WGS AF: 0.918 AC: 3194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.61
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4687587; hg19: chr3-53849510;