NM_001017372.3:c.482-3553_482-3551dupTAG

Variant names:

• chr5-128981579-C-CTAG
• rs1610859
• NM_001017372.3:c.482-3553_482-3551dupTAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001017372.3(SLC27A6):​c.482-3553_482-3551dupTAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 151,918 control chromosomes in the GnomAD database, including 1,235 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.077 (1235 hom., cov: 31)
• Consequence: SLC27A6 NM_001017372.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 2 publications found

Genes affected

SLC27A6 (HGNC:11000): (solute carrier family 27 member 6) This gene encodes a member of the fatty acid transport protein family (FATP). FATPs are involved in the uptake of long-chain fatty acids and have unique expression patterns. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017372.3. 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
	SLC27A6	NM_001017372.3	MANE Select	c.482-3553_482-3551dupTAG		intron	N/A	NP_001017372.1	Q9Y2P4
	SLC27A6	NM_001317984.2		c.482-3553_482-3551dupTAG		intron	N/A	NP_001304913.1	Q9Y2P4
	SLC27A6	NM_014031.5		c.482-3553_482-3551dupTAG		intron	N/A	NP_054750.1	Q9Y2P4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000262462.9	TSL:1 MANE Select	c.482-3554_482-3553insTAG		intron	N/A	ENSP00000262462.4	Q9Y2P4
	SLC27A6	ENST00000395266.5	TSL:1	c.482-3554_482-3553insTAG		intron	N/A	ENSP00000378684.1	Q9Y2P4
	SLC27A6	ENST00000506176.1	TSL:1	c.482-3554_482-3553insTAG		intron	N/A	ENSP00000421024.1	Q9Y2P4

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11627 AN: 151812 Hom.: 1235 Cov.: 31

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0766 AC: 11631 AN: 151918 Hom.: 1235 Cov.: 31 AF XY: 0.0822 AC XY: 6103 AN XY: 74220

African (AFR) AF: 0.0458 AC: 1900 AN: 41468

American (AMR) AF: 0.0999 AC: 1523 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2847 AN: 5092

South Asian (SAS) AF: 0.202 AC: 966 AN: 4790

European-Finnish (FIN) AF: 0.0598 AC: 631 AN: 10550

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.0488 AC: 3320 AN: 67992

Other (OTH) AF: 0.0751 AC: 158 AN: 2104

Alfa AF: 0.0543 Hom.: 57

Bravo AF: 0.0827

Asia WGS AF: 0.341 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1610859; hg19: chr5-128317272;