chr5-129020817-G-A

Variant names:

• chr5-129020817-G-A
• rs1148739
• NM_001017372.3:c.1165-2803G>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.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
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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.1165-2803G>A		intron	N/A	NP_001017372.1
	SLC27A6	NM_001317984.2		c.1165-2803G>A		intron	N/A	NP_001304913.1
	SLC27A6	NM_014031.5		c.1165-2803G>A		intron	N/A	NP_054750.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC27A6	ENST00000262462.9	TSL:1 MANE Select	c.1165-2803G>A		intron	N/A	ENSP00000262462.4
	SLC27A6	ENST00000395266.5	TSL:1	c.1165-2803G>A		intron	N/A	ENSP00000378684.1
	SLC27A6	ENST00000506176.1	TSL:1	c.1165-2803G>A		intron	N/A	ENSP00000421024.1

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

African (AFR) AF: 0.132 AC: 5479 AN: 41426

American (AMR) AF: 0.252 AC: 3847 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3468

East Asian (EAS) AF: 0.0425 AC: 219 AN: 5152

South Asian (SAS) AF: 0.187 AC: 900 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3087 AN: 10514

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23814 AN: 67896

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.164 Hom.: 420

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.31
PhyloP100		0.11
Mutation Taster		=100/0	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: rs1148739; hg19: chr5-128356510; COSMIC: COSV52481425; COSMIC: COSV52481425;