Variant 16-89098566-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001243279.3(ACSF3):c.-193-25C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 444,890 control chromosomes in the GnomAD database, including 3,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1802 hom., cov: 34)

Exomes 𝑓: 0.12 ( 2197 hom. )

Consequence

ACSF3
NM_001243279.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.174

Variant links:

Genes affected

ACSF3 (HGNC:27288): (acyl-CoA synthetase family member 3) This gene encodes a member of the acyl-CoA synthetase family of enzymes that activate fatty acids by catalyzing the formation of a thioester linkage between fatty acids and coenzyme A. The encoded protein is localized to mitochondria, has high specificity for malonate and methylmalonate and possesses malonyl-CoA synthetase activity. Mutations in this gene are a cause of combined malonic and methylmalonic aciduria. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Sep 2013]

ACSF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 16-89098566-C-A is Benign according to our data. Variant chr16-89098566-C-A is described in ClinVar as [Benign]. Clinvar id is 1294332.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSF3	NM_001243279.3 link	c.-193-25C>A		intron_variant	Intron 1 of 10	ENST00000614302.5	NP_001230208.1	Q4G176

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSF3	ENST00000614302.5 link	c.-193-25C>A		intron_variant	Intron 1 of 10	5	NM_001243279.3	ENSP00000479130.1		Q4G176

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22381

AN:

152148

Hom.:

1799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0246

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.131

GnomAD3 exomes

AF:

0.112

AC:

13999

AN:

125240

Hom.:

876

AF XY:

0.110

AC XY:

7528

AN XY:

68294

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.105

Gnomad EAS exome

AF:

0.0260

Gnomad SAS exome

AF:

0.104

Gnomad FIN exome

AF:

0.104

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.119

AC:

34695

AN:

292624

Hom.:

2197

Cov.:

AF XY:

0.116

AC XY:

19231

AN XY:

165838

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.110

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.0235

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.111

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.147

AC:

22404

AN:

152266

Hom.:

1802

Cov.:

AF XY:

0.144

AC XY:

10718

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.0251

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.127

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.135

Hom.:

269

Bravo

AF:

0.151

Asia WGS

AF:

0.0700

AC:

241

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.6

DANN

Benign

0.66

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over