Variant 20-25020047-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_032501.4(ACSS1):c.1209G>A(p.Lys403=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0085 in 1,614,220 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0075 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0086 ( 55 hom. )

Consequence

ACSS1
NM_032501.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.345

Variant links:

Genes affected

ACSS1 (HGNC:16091): (acyl-CoA synthetase short chain family member 1) This gene encodes a mitochondrial acetyl-CoA synthetase enzyme. A similar protein in mice plays an important role in the tricarboxylic acid cycle by catalyzing the conversion of acetate to acetyl CoA. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACSS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BP6

Variant 20-25020047-C-T is Benign according to our data. Variant chr20-25020047-C-T is described in ClinVar as [Benign]. Clinvar id is 2652247.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.345 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACSS1	NM_032501.4 linkuse as main transcript	c.1209G>A	p.Lys403=	synonymous_variant	7/14	ENST00000323482.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACSS1	ENST00000323482.9 linkuse as main transcript	c.1209G>A	p.Lys403=	synonymous_variant	7/14	1	NM_032501.4	P1	Q9NUB1-1
ACSS1	ENST00000432802.6 linkuse as main transcript	c.1209G>A	p.Lys403=	synonymous_variant	7/12	2			Q9NUB1-4
ACSS1	ENST00000537502.5 linkuse as main transcript	c.846G>A	p.Lys282=	synonymous_variant	6/13	2			Q9NUB1-3

Frequencies

GnomAD3 genomes

AF:

0.00747

AC:

1137

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00150

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0203

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00974

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00710

AC:

1785

AN:

251466

Hom.:

AF XY:

0.00700

AC XY:

951

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00945

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00176

Gnomad FIN exome

AF:

0.0153

Gnomad NFE exome

AF:

0.00854

Gnomad OTH exome

AF:

0.00977

GnomAD4 exome

AF:

0.00861

AC:

12588

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00839

AC XY:

6102

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.00164

Gnomad4 AMR exome

AF:

0.00932

Gnomad4 ASJ exome

AF:

0.00176

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00161

Gnomad4 FIN exome

AF:

0.0140

Gnomad4 NFE exome

AF:

0.00965

Gnomad4 OTH exome

AF:

0.00753

GnomAD4 genome

AF:

0.00746

AC:

1137

AN:

152352

Hom.:

Cov.:

AF XY:

0.00815

AC XY:

607

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00149

Gnomad4 AMR

AF:

0.00999

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0203

Gnomad4 NFE

AF:

0.00975

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00843

Hom.:

Bravo

AF:

0.00640

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00856

EpiControl

AF:

0.00936

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

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

ACSS1: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

6.5

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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