chr20-25007151-A-G

Variant names:

• chr20-25007151-A-G
• rs6132784
• ENST00000484396.1:n.3848T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484396.1(ACSS1):​n.3848T>C 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 0.164 in 1,320,066 control chromosomes in the GnomAD database, including 18,624 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 0.13 (1570 hom., cov: 33)
  • Exomes 𝑓: 0.17 (17054 hom.)
• Consequence: ACSS1 ENST00000484396.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 17 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484396.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSS1	NM_032501.4	MANE Select	c.*611T>C		3_prime_UTR	Exon 14 of 14	NP_115890.2
	ACSS1	NM_001252675.2		c.*611T>C		3_prime_UTR	Exon 14 of 14	NP_001239604.1
	ACSS1	NM_001252676.2		c.*611T>C		3_prime_UTR	Exon 13 of 13	NP_001239605.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSS1	ENST00000484396.1	TSL:1	n.3848T>C		non_coding_transcript_exon	Exon 2 of 2
	ACSS1	ENST00000323482.9	TSL:1 MANE Select	c.*611T>C		3_prime_UTR	Exon 14 of 14	ENSP00000316924.4
	ACSS1	ENST00000537502.5	TSL:2	c.*611T>C		3_prime_UTR	Exon 13 of 13	ENSP00000439304.2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20508 AN: 152140 Hom.: 1572 Cov.: 33

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.168 AC: 196476 AN: 1167808 Hom.: 17054 Cov.: 32 AF XY: 0.167 AC XY: 93533 AN XY: 558990

African (AFR) AF: 0.0741 AC: 1953 AN: 26342

American (AMR) AF: 0.116 AC: 1727 AN: 14924

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 3377 AN: 16052

East Asian (EAS) AF: 0.0701 AC: 2069 AN: 29532

South Asian (SAS) AF: 0.0878 AC: 3686 AN: 41990

European-Finnish (FIN) AF: 0.0989 AC: 2165 AN: 21892

Middle Eastern (MID) AF: 0.193 AC: 627 AN: 3254

European-Non Finnish (NFE) AF: 0.179 AC: 173109 AN: 966284

Other (OTH) AF: 0.163 AC: 7763 AN: 47538

GnomAD4 genome AF: 0.135 AC: 20506 AN: 152258 Hom.: 1570 Cov.: 33 AF XY: 0.130 AC XY: 9662 AN XY: 74450

African (AFR) AF: 0.0782 AC: 3252 AN: 41562

American (AMR) AF: 0.133 AC: 2038 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3470

East Asian (EAS) AF: 0.0642 AC: 333 AN: 5184

South Asian (SAS) AF: 0.0935 AC: 451 AN: 4824

European-Finnish (FIN) AF: 0.0868 AC: 921 AN: 10616

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12242 AN: 67988

Other (OTH) AF: 0.160 AC: 338 AN: 2116

Alfa AF: 0.158 Hom.: 1953

Bravo AF: 0.134

Asia WGS AF: 0.0970 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6132784; hg19: chr20-24987787;