chr5-128985309-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017372.3(SLC27A6):c.658C>T(p.Leu220Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000027 ( 0 hom. )
Consequence
SLC27A6
NM_001017372.3 missense
NM_001017372.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 0.394
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.038590103).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC27A6 | NM_001017372.3 | c.658C>T | p.Leu220Phe | missense_variant | 2/10 | ENST00000262462.9 | |
SLC27A6 | NM_001317984.2 | c.658C>T | p.Leu220Phe | missense_variant | 3/11 | ||
SLC27A6 | NM_014031.5 | c.658C>T | p.Leu220Phe | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC27A6 | ENST00000262462.9 | c.658C>T | p.Leu220Phe | missense_variant | 2/10 | 1 | NM_001017372.3 | P1 | |
SLC27A6 | ENST00000395266.5 | c.658C>T | p.Leu220Phe | missense_variant | 3/11 | 1 | P1 | ||
SLC27A6 | ENST00000506176.1 | c.658C>T | p.Leu220Phe | missense_variant | 3/11 | 1 | P1 | ||
SLC27A6 | ENST00000508645.5 | c.115C>T | p.Leu39Phe | missense_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152190Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
73
AN:
152190
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251274Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135804
GnomAD3 exomes
AF:
AC:
23
AN:
251274
Hom.:
AF XY:
AC XY:
9
AN XY:
135804
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727182
GnomAD4 exome
AF:
AC:
39
AN:
1461744
Hom.:
Cov.:
31
AF XY:
AC XY:
12
AN XY:
727182
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000486 AC: 74AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74480
GnomAD4 genome
?
AF:
AC:
74
AN:
152308
Hom.:
Cov.:
32
AF XY:
AC XY:
32
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
5
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
13
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.658C>T (p.L220F) alteration is located in exon 2 (coding exon 2) of the SLC27A6 gene. This alteration results from a C to T substitution at nucleotide position 658, causing the leucine (L) at amino acid position 220 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;.;.;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;D;D;D
Polyphen
0.87
.;P;P;P
Vest4
0.48, 0.48, 0.48
MVP
MPC
0.34
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at