rs1610859

Positions:

• chr5-128981579-C-CTAG

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC27A6	NM_001017372.3	c.482-3553_482-3551dupTAG		intron_variant		ENST00000262462.9	NP_001017372.1
SLC27A6	NM_001317984.2	c.482-3553_482-3551dupTAG		intron_variant			NP_001304913.1
SLC27A6	NM_014031.5	c.482-3553_482-3551dupTAG		intron_variant			NP_054750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC27A6	ENST00000262462.9	c.482-3553_482-3551dupTAG		intron_variant		1	NM_001017372.3	ENSP00000262462.4
SLC27A6	ENST00000395266.5	c.482-3553_482-3551dupTAG		intron_variant		1		ENSP00000378684.1
SLC27A6	ENST00000506176.1	c.482-3553_482-3551dupTAG		intron_variant		1		ENSP00000421024.1
SLC27A6	ENST00000508645.5	c.-62-3553_-62-3551dupTAG		intron_variant		5		ENSP00000421759.1

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

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.0999

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0598

Gnomad4 NFE AF: 0.0488

Gnomad4 OTH AF: 0.0751

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1610859; hg19: chr5-128317272;