rs632650

Variant names:

• chr12-111693894-G-T
• rs632650
• NM_025247.6:c.187+998G>T

Variant summary

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

The NM_025247.6(ACAD10):​c.187+998G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,124 control chromosomes in the GnomAD database, including 2,235 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 (2235 hom., cov: 32)
• Consequence: ACAD10 NM_025247.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 22 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025247.6. 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.187+998G>T		intron	N/A	NP_079523.3
	ACAD10	NM_001136538.2		c.187+998G>T		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.187+998G>T		intron	N/A	ENSP00000325137.5
	ACAD10	ENST00000455480.6	TSL:1	c.187+998G>T		intron	N/A	ENSP00000389813.2
	ACAD10	ENST00000507135.5	TSL:1	n.359+998G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25434 AN: 152006 Hom.: 2239 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.167 AC: 25430 AN: 152124 Hom.: 2235 Cov.: 32 AF XY: 0.167 AC XY: 12445 AN XY: 74362

African (AFR) AF: 0.187 AC: 7753 AN: 41506

American (AMR) AF: 0.166 AC: 2542 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 309 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5166

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4818

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10576

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10242 AN: 67998

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.158 Hom.: 3857

Bravo AF: 0.171

Asia WGS AF: 0.263 AC: 914 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	2.4
DANN	Benign	0.72
PhyloP100		0.23
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: rs632650; hg19: chr12-112131698;