5-131959599-C-G

Variant names:

• chr5-131959599-C-G
• NM_001009185.3:c.1968G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001009185.3(ACSL6):​c.1968G>C​(p.Lys656Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ACSL6 NM_001009185.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.727

Genes affected

ACSL6 (HGNC:16496): (acyl-CoA synthetase long chain family member 6) The protein encoded by this gene catalyzes the formation of acyl-CoA from fatty acids, ATP, and CoA, using magnesium as a cofactor. The encoded protein plays a major role in fatty acid metabolism in the brain. Translocations with the ETV6 gene are causes of myelodysplastic syndrome with basophilia, acute myelogenous leukemia with eosinophilia, and acute eosinophilic leukemia. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2011]

ENSG00000281938 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26682276).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSL6	NM_001009185.3	c.1968G>C	p.Lys656Asn	missense_variant	Exon 20 of 21	ENST00000651883.2	NP_001009185.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSL6	ENST00000651883.2	c.1968G>C	p.Lys656Asn	missense_variant	Exon 20 of 21		NM_001009185.3	ENSP00000499063.2
ENSG00000281938	ENST00000652469.1	n.1968G>C		non_coding_transcript_exon_variant	Exon 20 of 26			ENSP00000498837.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 05, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1968G>C (p.K656N) alteration is located in exon 20 (coding exon 20) of the ACSL6 gene. This alteration results from a G to C substitution at nucleotide position 1968, causing the lysine (K) at amino acid position 656 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.25	.;.;.;.;.;.;T;.;.
Eigen	Benign	0.0091
Eigen_PC	Benign	0.089
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.84	T;T;.;T;T;T;T;T;T
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.27	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.3	.;.;.;.;.;M;M;.;.
PrimateAI	Benign	0.45	T
PROVEAN	Uncertain	-4.1	D;D;D;D;D;D;D;.;D
REVEL	Benign	0.14
Sift	Uncertain	0.014	D;D;D;D;D;D;D;.;D
Sift4G	Uncertain	0.020	D;T;T;D;D;D;D;D;D
Polyphen		0.19	B;B;B;B;.;B;B;B;.
Vest4		0.45
MutPred		0.49		.;.;.;.;.;Gain of ubiquitination at K628 (P = 0.0388);Gain of ubiquitination at K628 (P = 0.0388);.;.;
MVP		0.59
MPC		0.69
ClinPred		0.97	D
GERP RS		4.1
Varity_R		0.56
gMVP		0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-131295292;