Variant rs7132509 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000313698.9(ACAD10):c.187+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 1,612,982 control chromosomes in the GnomAD database, including 11,792 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.078 ( 1618 hom., cov: 32)

Exomes 𝑓: 0.036 ( 10174 hom. )

Consequence

ACAD10
ENST00000313698.9 splice_region, intron

Scores

Splicing: ADA: 0.00003145

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.350

Variant links:

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]

ACAD10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACAD10	NM_025247.6 linkuse as main transcript	c.187+8A>G		splice_region_variant, intron_variant		ENST00000313698.9	NP_079523.3
ACAD10	NM_001136538.2 linkuse as main transcript	c.187+8A>G		splice_region_variant, intron_variant			NP_001130010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACAD10	ENST00000313698.9 linkuse as main transcript	c.187+8A>G		splice_region_variant, intron_variant		1	NM_025247.6	ENSP00000325137	P1	Q6JQN1-1

Frequencies

GnomAD3 genomes

AF:

0.0781

AC:

11870

AN:

151946

Hom.:

1620

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.621

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.00208

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.00357

Gnomad OTH

AF:

0.0824

GnomAD3 exomes

AF:

0.0971

AC:

24184

AN:

249034

Hom.:

4870

AF XY:

0.0873

AC XY:

11747

AN XY:

134552

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.185

Gnomad ASJ exome

AF:

0.00524

Gnomad EAS exome

AF:

0.654

Gnomad SAS exome

AF:

0.0792

Gnomad FIN exome

AF:

0.00368

Gnomad NFE exome

AF:

0.00395

Gnomad OTH exome

AF:

0.0560

GnomAD4 exome

AF:

0.0357

AC:

52181

AN:

1460918

Hom.:

10174

Cov.:

AF XY:

0.0358

AC XY:

26026

AN XY:

726750

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.175

Gnomad4 ASJ exome

AF:

0.00526

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.0798

Gnomad4 FIN exome

AF:

0.00334

Gnomad4 NFE exome

AF:

0.00262

Gnomad4 OTH exome

AF:

0.0574

GnomAD4 genome

AF:

0.0782

AC:

11892

AN:

152064

Hom.:

1618

Cov.:

AF XY:

0.0830

AC XY:

6170

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.117

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.00208

Gnomad4 NFE

AF:

0.00357

Gnomad4 OTH

AF:

0.0820

Alfa

AF:

0.0290

Hom.:

175

Bravo

AF:

0.0950

Asia WGS

AF:

0.260

AC:

902

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.7

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000031

dbscSNV1_RF

Benign

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over