ENST00000546840.3:c.102+1423C>A

Variant names:

• chr12-111757166-T-A
• ENST00000546840.3:c.102+1421T>A

Variant summary

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

The ENST00000546840.3(ENSG00000257767):​c.102+1421T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000257767 ENST00000546840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 0 publications found

Genes affected

ENSG00000257767 (HGNC:):

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: 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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546840.3. 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.*693T>A		downstream_gene	N/A	NP_079523.3
	ACAD10	NM_001136538.2		c.*693T>A		downstream_gene	N/A	NP_001130010.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257767	ENST00000546840.3	TSL:5	c.102+1421T>A		intron	N/A	ENSP00000450353.4
	ACAD10	ENST00000313698.9	TSL:1 MANE Select	c.*693T>A		downstream_gene	N/A	ENSP00000325137.5
	ACAD10	ENST00000455480.6	TSL:1	c.*693T>A		downstream_gene	N/A	ENSP00000389813.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 189078 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 103532

African (AFR) AF: 0.00 AC: 0 AN: 4838

American (AMR) AF: 0.00 AC: 0 AN: 9284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4268

East Asian (EAS) AF: 0.00 AC: 0 AN: 7244

South Asian (SAS) AF: 0.00 AC: 0 AN: 40014

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 660

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 105242

Other (OTH) AF: 0.00 AC: 0 AN: 8986

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.83
PhyloP100		0.23

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

hg19: chr12-112194970;