Variant 8-81529565-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001105281.6(FABP12):c.119C>T(p.Thr40Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FABP12
NM_001105281.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.643

Variant links:

Genes affected

FABP12 (HGNC:34524): (fatty acid binding protein 12) Predicted to enable lipid binding activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

FABP12 links:

FABP12 (HGNC:):

FABP12 links:

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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=0.1491887).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
FABP12	NM_001105281.6 linkuse as main transcript	c.119C>T	p.Thr40Ile	missense_variant	3/5	NP_001098751.1	A6NFH5
FABP12	XM_006716465.4 linkuse as main transcript	c.119C>T	p.Thr40Ile	missense_variant	3/5	XP_006716528.1	A6NFH5
FABP12	XM_011517577.3 linkuse as main transcript	c.119C>T	p.Thr40Ile	missense_variant	4/6	XP_011515879.1	A6NFH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
FABP12	ENST00000360464.6 linkuse as main transcript	c.119C>T	p.Thr40Ile	missense_variant	3/5	1	ENSP00000353650.4	A6NFH5
FABP12	ENST00000692030.1 linkuse as main transcript	c.119C>T	p.Thr40Ile	missense_variant	4/6		ENSP00000510293.1	A6NFH5
FABP12	ENST00000519696.1 linkuse as main transcript	n.71C>T		non_coding_transcript_exon_variant	2/4	5	ENSP00000427973.1	H0YAS1
ENSG00000253374	ENST00000523380.5 linkuse as main transcript	n.505+3109G>A		intron_variant		5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461590

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727078

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:

0.00

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

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

Aug 27, 2024

The c.119C>T (p.T40I) alteration is located in exon 2 (coding exon 2) of the FABP12 gene. This alteration results from a C to T substitution at nucleotide position 119, causing the threonine (T) at amino acid position 40 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

0.12

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.033

Eigen

Benign

-0.53

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.090

LIST_S2

Benign

0.28

M_CAP

Benign

0.0020

MetaRNN

Benign

0.15

MetaSVM

Benign

-0.99

MutationAssessor

Pathogenic

2.9

PrimateAI

Benign

0.26

PROVEAN

Uncertain

-3.6

REVEL

Benign

0.032

Sift

Benign

0.032

Sift4G

Uncertain

0.060

Polyphen

0.44

Vest4

0.16

MutPred

0.40

Loss of disorder (P = 0.0757);

MVP

0.061

MPC

0.0097

ClinPred

0.62

GERP RS

0.26

Varity_R

0.12

gMVP

0.39

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over