rs7132119

Positions:

• chr12-81155896-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548058.6(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 ENST00000548058.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ACSS3	NM_024560.4	c.1098+3800C>A		intron_variant		ENST00000548058.6	NP_078836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSS3	ENST00000548058.6	c.1098+3800C>A		intron_variant		1	NM_024560.4	ENSP00000449535	A1
ACSS3	ENST00000261206.7	c.1095+3800C>A		intron_variant		1		ENSP00000261206	P4
ACSS3	ENST00000548324.5	n.370+3800C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0947

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.341

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

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

Other links and lift over

dbSNP: rs7132119; hg19: chr12-81549675;