Variant 16-89093921-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001243279.3(ACSF3):c.-269C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 324,882 control chromosomes in the GnomAD database, including 6,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 2007 hom., cov: 32)

Exomes 𝑓: 0.19 ( 4446 hom. )

Consequence

ACSF3
NM_001243279.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.368

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 16-89093921-C-G is Benign according to our data. Variant chr16-89093921-C-G is described in ClinVar as [Benign]. Clinvar id is 1248015.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACSF3	NM_001243279.3 linkuse as main transcript	c.-269C>G		5_prime_UTR_variant	1/11	ENST00000614302.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACSF3	ENST00000614302.5 linkuse as main transcript	c.-269C>G		5_prime_UTR_variant	1/11	5	NM_001243279.3	P1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20282

AN:

149184

Hom.:

1992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0334

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0796

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.228

AC:

16471

AN:

72360

Hom.:

2815

AF XY:

0.211

AC XY:

8812

AN XY:

41854

show subpopulations

Gnomad AFR exome

AF:

0.0317

Gnomad AMR exome

AF:

0.509

Gnomad ASJ exome

AF:

0.130

Gnomad EAS exome

AF:

0.220

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.104

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.186

AC:

32674

AN:

175590

Hom.:

4446

Cov.:

AF XY:

0.182

AC XY:

19557

AN XY:

107464

show subpopulations

Gnomad4 AFR exome

AF:

0.0418

Gnomad4 AMR exome

AF:

0.496

Gnomad4 ASJ exome

AF:

0.124

Gnomad4 EAS exome

AF:

0.217

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.136

AC:

20305

AN:

149292

Hom.:

2007

Cov.:

AF XY:

0.139

AC XY:

10095

AN XY:

72796

show subpopulations

Gnomad4 AFR

AF:

0.0333

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.193

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.139

Alfa

AF:

0.0665

Hom.:

Bravo

AF:

0.150

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.36

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