Variant 5-128966562-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000262462.9(SLC27A6):c.425A>T(p.Asn142Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Consequence

SLC27A6
ENST00000262462.9 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0730

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]

SLC27A6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.074439585).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC27A6	NM_001017372.3 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	1/10	ENST00000262462.9	NP_001017372.1
SLC27A6	NM_001317984.2 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	2/11		NP_001304913.1
SLC27A6	NM_014031.5 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	2/11		NP_054750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
SLC27A6	ENST00000262462.9 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	1/10	1	NM_001017372.3	ENSP00000262462	P1
SLC27A6	ENST00000395266.5 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	2/11	1		ENSP00000378684	P1
SLC27A6	ENST00000506176.1 linkuse as main transcript	c.425A>T	p.Asn142Ile	missense_variant	2/11	1		ENSP00000421024	P1
SLC27A6	ENST00000508645.5 linkuse as main transcript	c.-62-18571A>T		intron_variant		5		ENSP00000421759

Frequencies

GnomAD3 genomes

AF:

0.00000658

AC:

AN:

152048

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000658

AC:

AN:

152048

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.0000242

Gnomad4 AMR

AF:

0.00

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

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

Jun 07, 2024

The c.425A>T (p.N142I) alteration is located in exon 1 (coding exon 1) of the SLC27A6 gene. This alteration results from a A to T substitution at nucleotide position 425, causing the asparagine (N) at amino acid position 142 to be replaced by an isoleucine (I). 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

0.10

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

6.1

DANN

Benign

0.94

DEOGEN2

Benign

0.12

T;T;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.095

LIST_S2

Benign

0.68

.;.;T

M_CAP

Benign

0.0098

MetaRNN

Benign

0.074

T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.9

L;L;L

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.24

PROVEAN

Uncertain

-3.4

D;D;D

REVEL

Benign

0.018

Sift

Uncertain

0.0050

D;D;D

Sift4G

Uncertain

0.025

D;D;D

Polyphen

0.023

B;B;B

Vest4

0.17

MutPred

0.50

Gain of catalytic residue at N142 (P = 0.0451);Gain of catalytic residue at N142 (P = 0.0451);Gain of catalytic residue at N142 (P = 0.0451);

MVP

0.17

MPC

0.061

ClinPred

0.27

GERP RS

-3.0

Varity_R

0.26

gMVP

0.23

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over