rs7132119

Variant names:

• chr12-81155896-C-A
• rs7132119
• NM_024560.4:c.1098+3800C>A

Variant summary

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

The NM_024560.4(ACSS3):​c.1098+3800C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,058 control chromosomes in the GnomAD database, including 8,729 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 0.30 (8729 hom., cov: 32)
• Consequence: ACSS3 NM_024560.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915
• Publications: 1 publications found

Genes affected

ACSS3 (HGNC:24723): (acyl-CoA synthetase short chain family member 3) Enables propionate-CoA ligase activity. Predicted to be involved in ketone body biosynthetic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSS3	NM_024560.4	c.1098+3800C>A		intron_variant	Intron 7 of 15	ENST00000548058.6	NP_078836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSS3	ENST00000548058.6	c.1098+3800C>A		intron_variant	Intron 7 of 15	1	NM_024560.4	ENSP00000449535.1
ACSS3	ENST00000261206.7	c.1095+3800C>A		intron_variant	Intron 7 of 15	1		ENSP00000261206.3
ACSS3	ENST00000548324.5	n.370+3800C>A		intron_variant	Intron 2 of 10	2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45968 AN: 151940 Hom.: 8729 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.345

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.302 AC: 45957 AN: 152058 Hom.: 8729 Cov.: 32 AF XY: 0.299 AC XY: 22184 AN XY: 74302

African (AFR) AF: 0.0947 AC: 3930 AN: 41500

American (AMR) AF: 0.328 AC: 5005 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1629 AN: 3472

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5182

South Asian (SAS) AF: 0.281 AC: 1357 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3863 AN: 10542

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28861 AN: 67950

Other (OTH) AF: 0.341 AC: 720 AN: 2114

Alfa AF: 0.353 Hom.: 1827

Bravo AF: 0.293

Asia WGS AF: 0.145 AC: 507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.65
PhyloP100		-0.92
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: rs7132119; hg19: chr12-81549675;