chr5-128966131-T-A

Variant names:

• chr5-128966131-T-A
• rs2526246
• NM_001017372.3:c.-7T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	NM_001017372.3	MANE Select	c.-7T>A		5_prime_UTR	Exon 1 of 10	NP_001017372.1
	SLC27A6	NM_001317984.2		c.-7T>A		5_prime_UTR	Exon 2 of 11	NP_001304913.1
	SLC27A6	NM_014031.5		c.-7T>A		5_prime_UTR	Exon 2 of 11	NP_054750.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000262462.9	TSL:1 MANE Select	c.-7T>A		5_prime_UTR	Exon 1 of 10	ENSP00000262462.4
	SLC27A6	ENST00000395266.5	TSL:1	c.-7T>A		5_prime_UTR	Exon 2 of 11	ENSP00000378684.1
	SLC27A6	ENST00000506176.1	TSL:1	c.-7T>A		5_prime_UTR	Exon 2 of 11	ENSP00000421024.1

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

GnomAD2 exomes AF: 0.283 AC: 51874 AN: 183568 AF XY: 0.290

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 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

African (AFR) AF: 0.175 AC: 5113 AN: 29140

American (AMR) AF: 0.216 AC: 6775 AN: 31294

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 7996 AN: 20370

East Asian (EAS) AF: 0.0763 AC: 2994 AN: 39230

South Asian (SAS) AF: 0.210 AC: 14932 AN: 71220

European-Finnish (FIN) AF: 0.295 AC: 14813 AN: 50152

Middle Eastern (MID) AF: 0.430 AC: 2159 AN: 5016

European-Non Finnish (NFE) AF: 0.376 AC: 404195 AN: 1076164

Other (OTH) AF: 0.331 AC: 18741 AN: 56692

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

African (AFR) AF: 0.185 AC: 7291 AN: 39330

American (AMR) AF: 0.273 AC: 4153 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3466

East Asian (EAS) AF: 0.0664 AC: 342 AN: 5154

South Asian (SAS) AF: 0.207 AC: 999 AN: 4830

European-Finnish (FIN) AF: 0.294 AC: 3108 AN: 10578

Middle Eastern (MID) AF: 0.389 AC: 112 AN: 288

European-Non Finnish (NFE) AF: 0.374 AC: 25417 AN: 67962

Other (OTH) AF: 0.322 AC: 670 AN: 2080

Alfa AF: 0.319 Hom.: 1013

Bravo AF: 0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		-0.081
Mutation Taster		=300/0	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: rs2526246; hg19: chr5-128301824; COSMIC: COSV52480680;