5-128966514-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001017372.3(SLC27A6):​c.377C>T​(p.Ala126Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,605,700 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 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

SLC27A6
NM_001017372.3 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.07
Variant links:
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 Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28831494).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC27A6NM_001017372.3 linkc.377C>T p.Ala126Val missense_variant Exon 1 of 10 ENST00000262462.9 NP_001017372.1 Q9Y2P4
SLC27A6NM_001317984.2 linkc.377C>T p.Ala126Val missense_variant Exon 2 of 11 NP_001304913.1 Q9Y2P4B2R8P6
SLC27A6NM_014031.5 linkc.377C>T p.Ala126Val missense_variant Exon 2 of 11 NP_054750.1 Q9Y2P4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC27A6ENST00000262462.9 linkc.377C>T p.Ala126Val missense_variant Exon 1 of 10 1 NM_001017372.3 ENSP00000262462.4 Q9Y2P4
SLC27A6ENST00000395266.5 linkc.377C>T p.Ala126Val missense_variant Exon 2 of 11 1 ENSP00000378684.1 Q9Y2P4
SLC27A6ENST00000506176.1 linkc.377C>T p.Ala126Val missense_variant Exon 2 of 11 1 ENSP00000421024.1 Q9Y2P4
SLC27A6ENST00000508645.5 linkc.-62-18619C>T intron_variant Intron 3 of 6 5 ENSP00000421759.1 D6RAJ2

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
18
AN:
152154
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000410
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000207
AC:
5
AN:
241404
Hom.:
0
AF XY:
0.0000153
AC XY:
2
AN XY:
130340
show subpopulations
Gnomad AFR exome
AF:
0.000124
Gnomad AMR exome
AF:
0.0000604
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000551
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000482
AC:
7
AN:
1453546
Hom.:
0
Cov.:
34
AF XY:
0.00000415
AC XY:
3
AN XY:
722704
show subpopulations
Gnomad4 AFR exome
AF:
0.000121
Gnomad4 AMR exome
AF:
0.0000230
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000333
GnomAD4 genome
AF:
0.000118
AC:
18
AN:
152154
Hom.:
0
Cov.:
33
AF XY:
0.000135
AC XY:
10
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.000410
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.0000945
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000247
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jul 03, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.377C>T (p.A126V) alteration is located in exon 1 (coding exon 1) of the SLC27A6 gene. This alteration results from a C to T substitution at nucleotide position 377, causing the alanine (A) at amino acid position 126 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.33
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.14
T;T;T
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.81
D
LIST_S2
Benign
0.84
.;.;T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.29
T;T;T
MetaSVM
Benign
-0.82
T
MutationAssessor
Uncertain
2.5
M;M;M
PrimateAI
Uncertain
0.54
T
PROVEAN
Uncertain
-2.5
D;D;D
REVEL
Benign
0.20
Sift
Benign
0.30
T;T;T
Sift4G
Benign
0.19
T;T;T
Polyphen
0.73
P;P;P
Vest4
0.22
MVP
0.70
MPC
0.12
ClinPred
0.54
D
GERP RS
4.2
Varity_R
0.27
gMVP
0.63

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs146020710; hg19: chr5-128302207; API