rs17415911

Variant names:

• chr15-50205097-A-G
• rs17415911
• NM_003645.4:c.848-142A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-50205097-A-G
• chr15-50205097-A-T

Variant summary

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

The NM_003645.4(SLC27A2):​c.848-142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 904,052 control chromosomes in the GnomAD database, including 11,316 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 0.12 (1387 hom., cov: 30)
  • Exomes 𝑓: 0.15 (9929 hom.)
• Consequence: SLC27A2 NM_003645.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 2 publications found

Genes affected

SLC27A2 (HGNC:10996): (solute carrier family 27 member 2) The protein encoded by this gene is an isozyme of 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. This isozyme activates long-chain, branched-chain and very-long-chain fatty acids containing 22 or more carbons to their CoA derivatives. It is expressed primarily in liver and kidney, and is present in both endoplasmic reticulum and peroxisomes, but not in mitochondria. Its decreased peroxisomal enzyme activity is in part responsible for the biochemical pathology in X-linked adrenoleukodystrophy. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC27A2	NM_003645.4	c.848-142A>G		intron_variant	Intron 3 of 9	ENST00000267842.10	NP_003636.2
SLC27A2	NM_001159629.2	c.689-142A>G		intron_variant	Intron 2 of 8		NP_001153101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC27A2	ENST00000267842.10	c.848-142A>G		intron_variant	Intron 3 of 9	1	NM_003645.4	ENSP00000267842.5
SLC27A2	ENST00000380902.8	c.689-142A>G		intron_variant	Intron 2 of 8	1		ENSP00000370289.4
SLC27A2	ENST00000544960.1	c.143-142A>G		intron_variant	Intron 4 of 10	2		ENSP00000444549.1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18416 AN: 151852 Hom.: 1387 Cov.: 30

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.155 AC: 116201 AN: 752086 Hom.: 9929 AF XY: 0.154 AC XY: 57921 AN XY: 375584

African (AFR) AF: 0.0501 AC: 873 AN: 17428

American (AMR) AF: 0.119 AC: 1943 AN: 16380

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 2766 AN: 13628

East Asian (EAS) AF: 0.000615 AC: 18 AN: 29248

South Asian (SAS) AF: 0.136 AC: 4657 AN: 34278

European-Finnish (FIN) AF: 0.0817 AC: 2590 AN: 31712

Middle Eastern (MID) AF: 0.188 AC: 452 AN: 2410

European-Non Finnish (NFE) AF: 0.171 AC: 98032 AN: 573774

Other (OTH) AF: 0.147 AC: 4870 AN: 33228

GnomAD4 genome AF: 0.121 AC: 18415 AN: 151966 Hom.: 1387 Cov.: 30 AF XY: 0.117 AC XY: 8721 AN XY: 74282

African (AFR) AF: 0.0533 AC: 2210 AN: 41486

American (AMR) AF: 0.136 AC: 2080 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.130 AC: 625 AN: 4808

European-Finnish (FIN) AF: 0.0665 AC: 699 AN: 10506

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11535 AN: 67962

Other (OTH) AF: 0.146 AC: 307 AN: 2104

Alfa AF: 0.127 Hom.: 1032

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17415911; hg19: chr15-50497294;