Variant 20-34882891-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_018677.4(ACSS2):c.276C>T(p.Phe92Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 1,612,964 control chromosomes in the GnomAD database, including 297,373 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 0.54 ( 23074 hom., cov: 32)

Exomes 𝑓: 0.61 ( 274299 hom. )

Consequence

ACSS2
NM_018677.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.707

Variant links:

Genes affected

ACSS2 (HGNC:15814): (acyl-CoA synthetase short chain family member 2) This gene encodes a cytosolic enzyme that catalyzes the activation of acetate for use in lipid synthesis and energy generation. The protein acts as a monomer and produces acetyl-CoA from acetate in a reaction that requires ATP. Expression of this gene is regulated by sterol regulatory element-binding proteins, transcription factors that activate genes required for the synthesis of cholesterol and unsaturated fatty acids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]

ACSS2 links:

ACSS2 (HGNC:):

ACSS2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP7

Synonymous conserved (PhyloP=0.707 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACSS2	NM_018677.4 linkuse as main transcript	c.276C>T	p.Phe92Phe	synonymous_variant	2/18	ENST00000360596.7	NP_061147.1	Q9NR19-1Q6DKJ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSS2	ENST00000360596.7 linkuse as main transcript	c.276C>T	p.Phe92Phe	synonymous_variant	2/18	1	NM_018677.4	ENSP00000353804.2		Q9NR19-1
ACSS2	ENST00000484354.1 linkuse as main transcript	c.252C>T	p.Phe84Phe	synonymous_variant	2/3	5		ENSP00000419167.1		C9JXD9

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82353

AN:

151862

Hom.:

23061

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.625

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.734

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.565

AC:

141629

AN:

250606

Hom.:

42552

AF XY:

0.585

AC XY:

79277

AN XY:

135480

show subpopulations

Gnomad AFR exome

AF:

0.450

Gnomad AMR exome

AF:

0.281

Gnomad ASJ exome

AF:

0.631

Gnomad EAS exome

AF:

0.481

Gnomad SAS exome

AF:

0.739

Gnomad FIN exome

AF:

0.608

Gnomad NFE exome

AF:

0.620

Gnomad OTH exome

AF:

0.575

GnomAD4 exome

AF:

0.608

AC:

887751

AN:

1460984

Hom.:

274299

Cov.:

AF XY:

0.613

AC XY:

445496

AN XY:

726788

show subpopulations

Gnomad4 AFR exome

AF:

0.444

Gnomad4 AMR exome

AF:

0.298

Gnomad4 ASJ exome

AF:

0.632

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.738

Gnomad4 FIN exome

AF:

0.604

Gnomad4 NFE exome

AF:

0.621

Gnomad4 OTH exome

AF:

0.601

GnomAD4 genome

AF:

0.542

AC:

82375

AN:

151980

Hom.:

23074

Cov.:

AF XY:

0.541

AC XY:

40215

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.422

Gnomad4 ASJ

AF:

0.625

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.733

Gnomad4 FIN

AF:

0.595

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.540

Alfa

AF:

0.597

Hom.:

68938

Bravo

AF:

0.517

Asia WGS

AF:

0.595

AC:

2073

AN:

3478

EpiCase

AF:

0.614

EpiControl

AF:

0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.66

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over