4-184763242-GGC-CGT

Variant names:

• chr4-184763242-GGC-CGT
• NM_001995.5:c.1444_1446delGCCinsACG
• ACSL1 p.Ala482Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001995.5(ACSL1):​c.1444_1446delGCCinsACG​(p.Ala482Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ACSL1 NM_001995.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.73
• Publications: 0 publications found

Genes affected

ACSL1 (HGNC:3569): (acyl-CoA synthetase long chain family member 1) The protein encoded by this gene is an isozyme of the long-chain fatty-acid-coenzyme A ligase family. Although differing in substrate specificity, subcellular localization, and tissue distribution, all isozymes of this family convert free long-chain fatty acids into fatty acyl-CoA esters, and thereby play a key role in lipid biosynthesis and fatty acid degradation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001995.5. 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
	ACSL1	NM_001995.5	MANE Select	c.1444_1446delGCCinsACG	p.Ala482Thr	missense	N/A	NP_001986.2
	ACSL1	NM_001286708.2		c.1444_1446delGCCinsACG	p.Ala482Thr	missense	N/A	NP_001273637.1	P33121-1
	ACSL1	NM_001286710.2		c.1444_1446delGCCinsACG	p.Ala482Thr	missense	N/A	NP_001273639.1	P33121-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSL1	ENST00000281455.7	TSL:1 MANE Select	c.1444_1446delGCCinsACG	p.Ala482Thr	missense	N/A	ENSP00000281455.2	P33121-1
	ACSL1	ENST00000504342.5	TSL:1	c.1444_1446delGCCinsACG	p.Ala482Thr	missense	N/A	ENSP00000425006.1	P33121-1
	ACSL1	ENST00000505492.2	TSL:1	c.1366_1368delGCCinsACG	p.Ala456Thr	missense	N/A	ENSP00000425640.2	H0Y9Z9

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.7

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

hg19: chr4-185684396;