5-128966131-T-A

Position:

• chr5-128966131-T-A

Variant summary

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

The NM_001017372.3(SLC27A6):​c.-7T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,529,046 control chromosomes in the GnomAD database, including 93,759 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 0.29 (7117 hom., cov: 32)
  • Exomes 𝑓: 0.35 (86642 hom.)
• Consequence: SLC27A6 NM_001017372.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC27A6	NM_001017372.3	c.-7T>A		5_prime_UTR_variant	1/10	ENST00000262462.9	NP_001017372.1
SLC27A6	NM_001317984.2	c.-7T>A		5_prime_UTR_variant	2/11		NP_001304913.1
SLC27A6	NM_014031.5	c.-7T>A		5_prime_UTR_variant	2/11		NP_054750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC27A6	ENST00000262462	c.-7T>A		5_prime_UTR_variant	1/10	1	NM_001017372.3	ENSP00000262462.4
SLC27A6	ENST00000395266	c.-7T>A		5_prime_UTR_variant	2/11	1		ENSP00000378684.1
SLC27A6	ENST00000506176	c.-7T>A		5_prime_UTR_variant	2/11	1		ENSP00000421024.1
SLC27A6	ENST00000508645.5	c.-62-19002T>A		intron_variant		5		ENSP00000421759.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 43828 AN: 149644 Hom.: 7119 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.327

GnomAD3 exomes AF: 0.283 AC: 51874 AN: 183568 Hom.: 8435 AF XY: 0.290 AC XY: 27960 AN XY: 96302

Gnomad AFR exome AF: 0.172

Gnomad AMR exome AF: 0.208

Gnomad ASJ exome AF: 0.385

Gnomad EAS exome AF: 0.0627

Gnomad SAS exome AF: 0.192

Gnomad FIN exome AF: 0.291

Gnomad NFE exome AF: 0.370

Gnomad OTH exome AF: 0.315

GnomAD4 exome AF: 0.346 AC: 477718 AN: 1379278 Hom.: 86642 Cov.: 35 AF XY: 0.345 AC XY: 233975 AN XY: 678588

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.216

Gnomad4 ASJ exome AF: 0.393

Gnomad4 EAS exome AF: 0.0763

Gnomad4 SAS exome AF: 0.210

Gnomad4 FIN exome AF: 0.295

Gnomad4 NFE exome AF: 0.376

Gnomad4 OTH exome AF: 0.331

GnomAD4 genome AF: 0.293 AC: 43820 AN: 149768 Hom.: 7117 Cov.: 32 AF XY: 0.285 AC XY: 20923 AN XY: 73286

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.322

Alfa AF: 0.319 Hom.: 1013

Bravo AF: 0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.73

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: rs2526246; hg19: chr5-128301824; COSMIC: COSV52480680;