rs7681334

Positions:

• chr4-184789705-G-A
• chr4-184789705-G-C
• chr4-184789705-G-T

Variant summary

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

The NM_001995.5(ACSL1):​c.196-974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,020 control chromosomes in the GnomAD database, including 20,610 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 0.51 (20610 hom., cov: 32)
• Consequence: ACSL1 NM_001995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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]

ACSL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACSL1	NM_001995.5	c.196-974C>T		intron_variant		ENST00000281455.7	NP_001986.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACSL1	ENST00000281455.7	c.196-974C>T		intron_variant		1	NM_001995.5	ENSP00000281455.2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77327 AN: 151902 Hom.: 20590 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.509 AC: 77379 AN: 152020 Hom.: 20610 Cov.: 32 AF XY: 0.512 AC XY: 38070 AN XY: 74314

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.542

Alfa AF: 0.504 Hom.: 24625

Bravo AF: 0.528

Asia WGS AF: 0.739 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.44

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: rs7681334; hg19: chr4-185710859;