12-111692395-G-C

Variant names:

• chr12-111692395-G-C
• rs659964
• NM_025247.6:c.-13-302G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025247.6(ACAD10):​c.-13-302G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,186 control chromosomes in the GnomAD database, including 2,285 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 0.17 (2285 hom., cov: 32)
• Consequence: ACAD10 NM_025247.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

Genes affected

ACAD10 (HGNC:21597): (acyl-CoA dehydrogenase family member 10) This gene encodes a member of the acyl-CoA dehydrogenase family of enzymes (ACADs), which participate in the beta-oxidation of fatty acids in mitochondria. The encoded enzyme contains a hydrolase domain at the N-terminal portion, a serine/threonine protein kinase catlytic domain in the central region, and a conserved ACAD domain at the C-terminus. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACAD10	NM_025247.6	c.-13-302G>C		intron_variant	Intron 1 of 20	ENST00000313698.9	NP_079523.3
ACAD10	NM_001136538.2	c.-13-302G>C		intron_variant	Intron 1 of 21		NP_001130010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACAD10	ENST00000313698.9	c.-13-302G>C		intron_variant	Intron 1 of 20	1	NM_025247.6	ENSP00000325137.5

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25679 AN: 152068 Hom.: 2289 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.169 AC: 25676 AN: 152186 Hom.: 2285 Cov.: 32 AF XY: 0.169 AC XY: 12566 AN XY: 74384

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.183

Alfa AF: 0.0772 Hom.: 99

Bravo AF: 0.172

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.65

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

LitVar

Other links and lift over

dbSNP: rs659964; hg19: chr12-112130199;