rs6114999

Variant names:

• chr20-25007446-C-T
• rs6114999
• NM_032501.4:c.*316G>A

Variant summary

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

The NM_032501.4(ACSS1):​c.*316G>A variant causes a 3 prime UTR 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 NM_032501.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032501.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSS1	NM_032501.4	MANE Select	c.*316G>A		3_prime_UTR	Exon 14 of 14	NP_115890.2
	ACSS1	NM_001252675.2		c.*316G>A		3_prime_UTR	Exon 14 of 14	NP_001239604.1	Q9NUB1-2
	ACSS1	NM_001252676.2		c.*316G>A		3_prime_UTR	Exon 13 of 13	NP_001239605.1	Q9NUB1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSS1	ENST00000323482.9	TSL:1 MANE Select	c.*316G>A		3_prime_UTR	Exon 14 of 14	ENSP00000316924.4	Q9NUB1-1
	ACSS1	ENST00000484396.1	TSL:1	n.3553G>A		non_coding_transcript_exon	Exon 2 of 2
	ACSS1	ENST00000964866.1		c.*316G>A		3_prime_UTR	Exon 15 of 15	ENSP00000634925.1

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14818 AN: 152182 Hom.: 801 Cov.: 33

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.: 32 AF XY: 0.104 AC XY: 51149 AN XY: 492428

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: 12 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

GnomAD4 genome AF: 0.0974 AC: 14833 AN: 152300 Hom.: 802 Cov.: 33 AF XY: 0.0937 AC XY: 6975 AN XY: 74470

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: 10 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: 31 AN: 290

European-Non Finnish (NFE) AF: 0.107 AC: 7289 AN: 68022

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.27
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: rs6114999; hg19: chr20-24988082;