chr5-131956163-A-G

Variant names:

• chr5-131956163-A-G
• rs615305
• NM_001009185.3:c.2032-1792T>C

Variant summary

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

The NM_001009185.3(ACSL6):​c.2032-1792T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,066 control chromosomes in the GnomAD database, including 3,840 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 0.22 (3840 hom., cov: 32)
• Consequence: ACSL6 NM_001009185.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACSL6	NM_001009185.3	c.2032-1792T>C		intron_variant	Intron 20 of 20	ENST00000651883.2	NP_001009185.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACSL6	ENST00000651883.2	c.2032-1792T>C		intron_variant	Intron 20 of 20		NM_001009185.3	ENSP00000499063.2
ENSG00000281938	ENST00000652469.1	n.2031+3373T>C		intron_variant	Intron 20 of 25			ENSP00000498837.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32793 AN: 151948 Hom.: 3834 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.216 AC: 32827 AN: 152066 Hom.: 3840 Cov.: 32 AF XY: 0.222 AC XY: 16497 AN XY: 74314

African (AFR) AF: 0.172 AC: 7125 AN: 41494

American (AMR) AF: 0.252 AC: 3847 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.514 AC: 2652 AN: 5164

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4810

European-Finnish (FIN) AF: 0.283 AC: 2978 AN: 10532

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13317 AN: 68006

Other (OTH) AF: 0.206 AC: 435 AN: 2108

Alfa AF: 0.206 Hom.: 1147

Bravo AF: 0.214

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.33
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: rs615305; hg19: chr5-131291856;