dbSNP rs6114999: ACSS1:n.3553G>A (chr20-25007446-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000484396.1(ACSS1):n.3553G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,194,314 control chromosomes in the GnomAD database, including 6,810 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.097 ( 802 hom., cov: 33)

Exomes 𝑓: 0.10 ( 6008 hom. )

Consequence

ACSS1
ENST00000484396.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Publications

7 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSS1	NM_032501.4 link	c.*316G>A		3_prime_UTR_variant	Exon 14 of 14	ENST00000323482.9	NP_115890.2	Q9NUB1-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ACSS1	ENST00000484396.1 link	n.3553G>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
ACSS1	ENST00000323482.9 link	c.*316G>A	3_prime_UTR_variant	Exon 14 of 14	1	NM_032501.4	ENSP00000316924.4	Q9NUB1-1
ACSS1	ENST00000537502.5 link	c.*316G>A	3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000439304.2	Q9NUB1-3
ACSS1	ENST00000432802.6 link	c.1663-521G>A	intron_variant	Intron 11 of 11	2		ENSP00000388793.2	Q9NUB1-4

Frequencies

GnomAD3 genomes

AF:

0.0974

AC:

14818

AN:

152182

Hom.:

801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0805

Gnomad ASJ

AF:

0.0657

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0962

Gnomad FIN

AF:

0.0625

Gnomad MID

AF:

0.0929

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0936

GnomAD4 exome

AF:

0.104

AC:

108849

AN:

1042014

Hom.:

6008

Cov.:

AF XY:

0.104

AC XY:

51149

AN XY:

492428

show subpopulations

African (AFR)

AF:

0.113

AC:

2576

AN:

22720

American (AMR)

AF:

0.0567

AC:

503

AN:

8864

Ashkenazi Jewish (ASJ)

AF:

0.0554

AC:

671

AN:

12122

East Asian (EAS)

AF:

0.000684

AC:

AN:

17548

South Asian (SAS)

AF:

0.0835

AC:

2860

AN:

34270

European-Finnish (FIN)

AF:

0.0683

AC:

853

AN:

12482

Middle Eastern (MID)

AF:

0.108

AC:

279

AN:

2580

European-Non Finnish (NFE)

AF:

0.109

AC:

97306

AN:

891292

Other (OTH)

AF:

0.0944

AC:

3789

AN:

40136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

5648

11295

16943

22590

28238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4248

8496

12744

16992

21240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0974

AC:

14833

AN:

152300

Hom.:

802

Cov.:

AF XY:

0.0937

AC XY:

6975

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.112

AC:

4650

AN:

41560

American (AMR)

AF:

0.0803

AC:

1229

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0657

AC:

228

AN:

3472

East Asian (EAS)

AF:

0.00193

AC:

AN:

5182

South Asian (SAS)

AF:

0.0959

AC:

463

AN:

4828

European-Finnish (FIN)

AF:

0.0625

AC:

663

AN:

10614

Middle Eastern (MID)

AF:

0.107

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.107

AC:

7289

AN:

68022

Other (OTH)

AF:

0.0936

AC:

198

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

690

1380

2070

2760

3450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.103

Hom.:

274

Bravo

AF:

0.0985

Asia WGS

AF:

0.0590

AC:

207

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

2.1

(source)

DANN

Benign

0.68

PhyloP100

-0.27

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over