NM_001445.3:c.236C>A

Variant names:

• chr5-160232266-C-A
• NM_001445.3:c.236C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.42

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]

ACMG classification

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
FABP6	NM_001445.3	c.236C>A	p.Thr79Lys	missense_variant	Exon 2 of 4	ENST00000402432.4	NP_001436.1
FABP6	NM_001040442.1	c.383C>A	p.Thr128Lys	missense_variant	Exon 4 of 6		NP_001035532.1
FABP6	NM_001130958.2	c.383C>A	p.Thr128Lys	missense_variant	Exon 5 of 7		NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000402432.4	c.236C>A	p.Thr79Lys	missense_variant	Exon 2 of 4	1	NM_001445.3	ENSP00000385433.4

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

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;