rs1802536

Variant names:

• chr15-50236217-C-A
• rs1802536
• NM_003645.4:c.*121C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-50236217-C-A
• chr15-50236217-C-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.*121C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 743,338 control chromosomes in the GnomAD database, including 8,246 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 0.16 (2019 hom., cov: 32)
  • Exomes 𝑓: 0.14 (6227 hom.)
• Consequence: SLC27A2 NM_003645.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003645.4. 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
	SLC27A2	NM_003645.4	MANE Select	c.*121C>A		3_prime_UTR	Exon 10 of 10	NP_003636.2	O14975-1
	SLC27A2	NM_001159629.2		c.*121C>A		3_prime_UTR	Exon 9 of 9	NP_001153101.1	O14975-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A2	ENST00000267842.10	TSL:1 MANE Select	c.*121C>A		3_prime_UTR	Exon 10 of 10	ENSP00000267842.5	O14975-1
	SLC27A2	ENST00000380902.8	TSL:1	c.*121C>A		3_prime_UTR	Exon 9 of 9	ENSP00000370289.4	O14975-2
	SLC27A2	ENST00000895509.1		c.*121C>A		3_prime_UTR	Exon 11 of 11	ENSP00000565568.1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24135 AN: 151962 Hom.: 2019 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.140 AC: 82596 AN: 591258 Hom.: 6227 Cov.: 8 AF XY: 0.139 AC XY: 41930 AN XY: 302142

African (AFR) AF: 0.215 AC: 3073 AN: 14272

American (AMR) AF: 0.116 AC: 2133 AN: 18430

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 2002 AN: 13504

East Asian (EAS) AF: 0.0178 AC: 544 AN: 30580

South Asian (SAS) AF: 0.0885 AC: 2682 AN: 30314

European-Finnish (FIN) AF: 0.150 AC: 5368 AN: 35704

Middle Eastern (MID) AF: 0.166 AC: 361 AN: 2180

European-Non Finnish (NFE) AF: 0.149 AC: 62100 AN: 416730

Other (OTH) AF: 0.147 AC: 4333 AN: 29544

GnomAD4 genome AF: 0.159 AC: 24151 AN: 152080 Hom.: 2019 Cov.: 32 AF XY: 0.157 AC XY: 11644 AN XY: 74326

African (AFR) AF: 0.205 AC: 8504 AN: 41460

American (AMR) AF: 0.139 AC: 2127 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 512 AN: 3472

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5186

South Asian (SAS) AF: 0.0717 AC: 346 AN: 4828

European-Finnish (FIN) AF: 0.147 AC: 1554 AN: 10546

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10432 AN: 67984

Other (OTH) AF: 0.144 AC: 304 AN: 2114

Alfa AF: 0.114 Hom.: 292

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.34
PhyloP100		-0.22
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: rs1802536; hg19: chr15-50528414;