rs1148739

Positions:

• chr5-129020817-G-A
• chr5-129020817-G-C
• chr5-129020817-G-T

Variant summary

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

The NM_001017372.3(SLC27A6):​c.1165-2803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,820 control chromosomes in the GnomAD database, including 5,992 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 0.26 (5992 hom., cov: 31)
• Consequence: SLC27A6 NM_001017372.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC27A6	NM_001017372.3	c.1165-2803G>A		intron_variant		ENST00000262462.9	NP_001017372.1
SLC27A6	NM_001317984.2	c.1165-2803G>A		intron_variant			NP_001304913.1
SLC27A6	NM_014031.5	c.1165-2803G>A		intron_variant			NP_054750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC27A6	ENST00000262462.9	c.1165-2803G>A		intron_variant		1	NM_001017372.3	ENSP00000262462	P1
SLC27A6	ENST00000395266.5	c.1165-2803G>A		intron_variant		1		ENSP00000378684	P1
SLC27A6	ENST00000506176.1	c.1165-2803G>A		intron_variant		1		ENSP00000421024	P1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39471 AN: 151702 Hom.: 5984 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.260 AC: 39486 AN: 151820 Hom.: 5992 Cov.: 31 AF XY: 0.256 AC XY: 18990 AN XY: 74190

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.282

Alfa AF: 0.165 Hom.: 409

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.31

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: rs1148739; hg19: chr5-128356510; COSMIC: COSV52481425; COSMIC: COSV52481425;