5-41870495-C-A

Variant names:

• chr5-41870495-C-A
• rs865783219
• ENST00000972071.1:c.-137G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000972071.1(OXCT1):​c.-137G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 550,940 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: OXCT1 ENST00000972071.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.761
• Publications: 0 publications found

Genes affected

OXCT1 (HGNC:8527): (3-oxoacid CoA-transferase 1) This gene encodes a member of the 3-oxoacid CoA-transferase gene family. The encoded protein is a homodimeric mitochondrial matrix enzyme that plays a central role in extrahepatic ketone body catabolism by catalyzing the reversible transfer of coenzyme A from succinyl-CoA to acetoacetate. Mutations in this gene are associated with succinyl CoA:3-oxoacid CoA transferase deficiency. [provided by RefSeq, Jul 2008]

OXCT1-AS1 (HGNC:40423): (OXCT1 antisense RNA 1)

LOC102723752 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000972071.1. 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
	OXCT1-AS1	NR_046635.1		n.255+113C>A		intron	N/A
	OXCT1	NM_000436.4	MANE Select	c.-137G>T		upstream_gene	N/A	NP_000427.1	P55809-1
	OXCT1	NM_001364299.2		c.-137G>T		upstream_gene	N/A	NP_001351228.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXCT1	ENST00000972071.1		c.-137G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 18	ENSP00000642130.1
	OXCT1	ENST00000972069.1		c.-137G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	ENSP00000642128.1
	OXCT1	ENST00000899738.1		c.-137G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	ENSP00000569797.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000182 AC: 1 AN: 550940 Hom.: 0 Cov.: 6 AF XY: 0.00000338 AC XY: 1 AN XY: 296076

African (AFR) AF: 0.00 AC: 0 AN: 15426

American (AMR) AF: 0.00 AC: 0 AN: 33216

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19044

East Asian (EAS) AF: 0.00 AC: 0 AN: 31814

South Asian (SAS) AF: 0.00 AC: 0 AN: 60516

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2394

European-Non Finnish (NFE) AF: 0.00000307 AC: 1 AN: 325284

Other (OTH) AF: 0.00 AC: 0 AN: 30022

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.3
DANN	Benign	0.58
PhyloP100		0.76
PromoterAI		-0.21	Neutral

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: rs865783219; hg19: chr5-41870597;