Variant 19-6183147-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_030924.5(ACSBG2):c.1197G>A(p.Ala399=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,614,166 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0041 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0056 ( 37 hom. )

Consequence

ACSBG2
NM_030924.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.88

Variant links:

Genes affected

ACSBG2 (HGNC:24174): (acyl-CoA synthetase bubblegum family member 2) Enables acyl-CoA hydrolase activity and arachidonate-CoA ligase activity. Acts upstream of or within fatty acid metabolic process. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACSBG2 links:

LOC105372255 (HGNC:):

LOC105372255 links:

RFX2 (HGNC:9983): (regulatory factor X2) This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]

RFX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 19-6183147-G-A is Benign according to our data. Variant chr19-6183147-G-A is described in ClinVar as [Benign]. Clinvar id is 784712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.88 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 37 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACSBG2	NM_030924.5 linkuse as main transcript	c.1197G>A	p.Ala399=	synonymous_variant	10/15	ENST00000588485.6	NP_112186.3
LOC105372255	XR_936282.3 linkuse as main transcript	n.50-6704C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSBG2	ENST00000588485.6 linkuse as main transcript	c.1197G>A	p.Ala399=	synonymous_variant	10/15	1	NM_030924.5	ENSP00000466336	P1	Q5FVE4-1

Frequencies

GnomAD3 genomes

AF:

0.00413

AC:

628

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000845

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00705

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00629

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00481

AC:

1210

AN:

251410

Hom.:

AF XY:

0.00528

AC XY:

717

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.000984

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.0109

Gnomad FIN exome

AF:

0.00430

Gnomad NFE exome

AF:

0.00573

Gnomad OTH exome

AF:

0.00440

GnomAD4 exome

AF:

0.00558

AC:

8160

AN:

1461876

Hom.:

Cov.:

AF XY:

0.00587

AC XY:

4271

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.00127

Gnomad4 ASJ exome

AF:

0.00260

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0102

Gnomad4 FIN exome

AF:

0.00376

Gnomad4 NFE exome

AF:

0.00599

Gnomad4 OTH exome

AF:

0.00392

GnomAD4 genome

AF:

0.00414

AC:

630

AN:

152290

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

298

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000842

Gnomad4 AMR

AF:

0.00432

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00726

Gnomad4 FIN

AF:

0.00443

Gnomad4 NFE

AF:

0.00629

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00583

Hom.:

Bravo

AF:

0.00342

Asia WGS

AF:

0.00491

AC:

AN:

3478

EpiCase

AF:

0.00540

EpiControl

AF:

0.00456

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 02, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.20

DANN

Benign

0.32

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