12-111752634-C-A

Variant names:

• chr12-111752634-C-A
• rs6490294
• NM_025247.6:c.2818-1138C>A

Variant summary

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

The NM_001136538.2(ACAD10):​c.2911-1138C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,578 control chromosomes in the GnomAD database, including 13,965 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 0.35 (13965 hom., cov: 30)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: ACAD10 NM_001136538.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 35 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136538.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACAD10	NM_025247.6	MANE Select	c.2818-1138C>A		intron	N/A	NP_079523.3
	ACAD10	NM_001136538.2		c.2911-1138C>A		intron	N/A	NP_001130010.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACAD10	ENST00000313698.9	TSL:1 MANE Select	c.2818-1138C>A		intron	N/A	ENSP00000325137.5
	ACAD10	ENST00000455480.6	TSL:1	c.2911-1138C>A		intron	N/A	ENSP00000389813.2
	ACAD10	ENST00000893914.1		c.3049-1138C>A		intron	N/A	ENSP00000563973.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53645 AN: 151446 Hom.: 13925 Cov.: 30

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.188 AC: 3 AN: 16 Hom.: 0 AF XY: 0.167 AC XY: 2 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.355 AC: 53746 AN: 151562 Hom.: 13965 Cov.: 30 AF XY: 0.354 AC XY: 26255 AN XY: 74074

African (AFR) AF: 0.681 AC: 28124 AN: 41316

American (AMR) AF: 0.329 AC: 4994 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 348 AN: 3458

East Asian (EAS) AF: 0.855 AC: 4407 AN: 5156

South Asian (SAS) AF: 0.317 AC: 1519 AN: 4794

European-Finnish (FIN) AF: 0.154 AC: 1624 AN: 10514

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11797 AN: 67850

Other (OTH) AF: 0.333 AC: 697 AN: 2096

Alfa AF: 0.245 Hom.: 20928

Bravo AF: 0.388

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		0.19
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: rs6490294; hg19: chr12-112190438;