3-38137763-C-A

Variant names:

• chr3-38137763-C-A
• rs4988453
• ENST00000760417.1:n.1515G>T

Variant summary

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

The ENST00000760417.1(ENSG00000299092):​n.1515G>T 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 0.0569 in 152,258 control chromosomes in the GnomAD database, including 274 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 0.057 (274 hom., cov: 33)
• Consequence: ENSG00000299092 ENST00000760417.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 27 publications found

Genes affected

ENSG00000299092 (HGNC:):

ACAA1 (HGNC:82): (acetyl-CoA acyltransferase 1) This gene encodes an enzyme operative in the beta-oxidation system of the peroxisomes. Deficiency of this enzyme leads to pseudo-Zellweger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760417.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299092	ENST00000760417.1		n.1515G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000299114	ENST00000760536.1		n.351C>A		non_coding_transcript_exon	Exon 1 of 1
	ACAA1	ENST00000955504.1		c.-556G>T		upstream_gene	N/A	ENSP00000625563.1

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8647 AN: 152140 Hom.: 274 Cov.: 33

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0569 AC: 8659 AN: 152258 Hom.: 274 Cov.: 33 AF XY: 0.0576 AC XY: 4288 AN XY: 74448

African (AFR) AF: 0.0857 AC: 3559 AN: 41538

American (AMR) AF: 0.0432 AC: 661 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5186

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4832

European-Finnish (FIN) AF: 0.0814 AC: 864 AN: 10610

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0462 AC: 3140 AN: 68006

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

Alfa AF: 0.0393 Hom.: 80

Bravo AF: 0.0555

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.5
DANN	Benign	0.77
PhyloP100		0.0090

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4988453;

hg19: chr3-38179254;