rs257906

Variant names:

• chr5-129001330-C-T
• rs257906
• NM_001017372.3:c.969+10866C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.95).
• 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 rank	MANE	Protein	UniProt
SLC27A6	NM_001017372.3	c.969+10866C>T		intron_variant	Intron 4 of 9	ENST00000262462.9	NP_001017372.1
SLC27A6	NM_001317984.2	c.969+10866C>T		intron_variant	Intron 5 of 10		NP_001304913.1
SLC27A6	NM_014031.5	c.969+10866C>T		intron_variant	Intron 5 of 10		NP_054750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC27A6	ENST00000262462.9	c.969+10866C>T		intron_variant	Intron 4 of 9	1	NM_001017372.3	ENSP00000262462.4
SLC27A6	ENST00000395266.5	c.969+10866C>T		intron_variant	Intron 5 of 10	1		ENSP00000378684.1
SLC27A6	ENST00000506176.1	c.969+10866C>T		intron_variant	Intron 5 of 10	1		ENSP00000421024.1
SLC27A6	ENST00000508645.5	c.426+10866C>T		intron_variant	Intron 6 of 6	5		ENSP00000421759.1

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

African (AFR) AF: 0.251 AC: 10414 AN: 41462

American (AMR) AF: 0.333 AC: 5089 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3638 AN: 5160

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1940 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10760 AN: 67986

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.183 Hom.: 1692

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
PhyloP100		0.28
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: rs257906; hg19: chr5-128337023;