rs1130435

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001445.3(FABP6):​c.236C>A​(p.Thr79Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000207 in 1,451,796 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T79M) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

FABP6
NM_001445.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.42
Variant links:
Genes affected
FABP6 (HGNC:3561): (fatty acid binding protein 6) This gene encodes the ileal fatty acid binding protein. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. FABP6 and FABP1 (the liver fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. Transcript variants generated by alternate transcription promoters and/or alternate splicing have been found for this gene. [provided by RefSeq, Jul 2008]

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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=0.048840284).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FABP6NM_001445.3 linkc.236C>A p.Thr79Lys missense_variant Exon 2 of 4 ENST00000402432.4 NP_001436.1 P51161-1
FABP6NM_001040442.1 linkc.383C>A p.Thr128Lys missense_variant Exon 4 of 6 NP_001035532.1 P51161-2
FABP6NM_001130958.2 linkc.383C>A p.Thr128Lys missense_variant Exon 5 of 7 NP_001124430.1 P51161-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FABP6ENST00000402432.4 linkc.236C>A p.Thr79Lys missense_variant Exon 2 of 4 1 NM_001445.3 ENSP00000385433.4 P51161-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000207
AC:
3
AN:
1451796
Hom.:
0
Cov.:
36
AF XY:
0.00000277
AC XY:
2
AN XY:
721390
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000189
Gnomad4 NFE exome
AF:
0.00000181
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
15
DANN
Benign
0.31
DEOGEN2
Benign
0.042
.;T
Eigen
Benign
-0.99
Eigen_PC
Benign
-0.72
FATHMM_MKL
Benign
0.23
N
LIST_S2
Benign
0.62
T;T
M_CAP
Benign
0.0033
T
MetaRNN
Benign
0.049
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
-3.2
.;N
PrimateAI
Benign
0.40
T
PROVEAN
Benign
5.6
N;N
REVEL
Benign
0.072
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;B
Vest4
0.14
MutPred
0.47
.;Gain of methylation at T79 (P = 0.0184);
MVP
0.12
MPC
0.20
ClinPred
0.14
T
GERP RS
3.5
Varity_R
0.41
gMVP
0.43

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-159659273; API