rs257906

chr5-129001330-C-T

Variant summary

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

The NM_001017372.3(SLC27A6):c.969+10866C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,064 control chromosomes in the GnomAD database, including 5,135 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 0.23 (5135 hom., cov: 33)
• Consequence: SLC27A6 NM_001017372.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC27A6	NM_001017372.3	c.969+10866C>T		intron_variant		ENST00000262462.9
SLC27A6	NM_001317984.2	c.969+10866C>T		intron_variant
SLC27A6	NM_014031.5	c.969+10866C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC27A6	ENST00000262462.9	c.969+10866C>T		intron_variant		1	NM_001017372.3	P1
SLC27A6	ENST00000395266.5	c.969+10866C>T		intron_variant		1		P1
SLC27A6	ENST00000506176.1	c.969+10866C>T		intron_variant		1		P1
SLC27A6	ENST00000508645.5	c.426+10866C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34933 AN: 151946 Hom.: 5124 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.230 AC: 34979 AN: 152064 Hom.: 5135 Cov.: 33 AF XY: 0.239 AC XY: 17763 AN XY: 74324

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.224

Alfa AF: 0.183 Hom.: 1542

Bravo AF: 0.246

Asia WGS AF: 0.553 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.5
Dann	Benign	0.81

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: rs257906; hg19: chr5-128337023;