Variant 8-81529605-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001105281.6(FABP12):c.79G>C(p.Gly27Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,132 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

FABP12
NM_001105281.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.81

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 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
FABP12	NM_001105281.6 linkuse as main transcript	c.79G>C	p.Gly27Arg	missense_variant	3/5	NP_001098751.1	A6NFH5
FABP12	XM_006716465.4 linkuse as main transcript	c.79G>C	p.Gly27Arg	missense_variant	3/5	XP_006716528.1	A6NFH5
FABP12	XM_011517577.3 linkuse as main transcript	c.79G>C	p.Gly27Arg	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.79G>C	p.Gly27Arg	missense_variant	3/5	1	ENSP00000353650.4	A6NFH5
FABP12	ENST00000692030.1 linkuse as main transcript	c.79G>C	p.Gly27Arg	missense_variant	4/6		ENSP00000510293.1	A6NFH5
FABP12	ENST00000519696.1 linkuse as main transcript	n.31G>C		non_coding_transcript_exon_variant	2/4	5	ENSP00000427973.1	H0YAS1
ENSG00000253374	ENST00000523380.5 linkuse as main transcript	n.505+3149C>G		intron_variant		5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000403

AC:

AN:

248092

Hom.:

AF XY:

0.00

AC XY:

AN XY:

134538

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000292

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

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:

0.00000274

AC:

AN:

1460132

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726302

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000900

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:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000113

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 16, 2024

The c.79G>C (p.G27R) alteration is located in exon 2 (coding exon 2) of the FABP12 gene. This alteration results from a G to C substitution at nucleotide position 79, causing the glycine (G) at amino acid position 27 to be replaced by an arginine (R). 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

0.25

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.044

Eigen

Benign

-0.015

Eigen_PC

Benign

-0.061

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.80

M_CAP

Benign

0.012

MetaRNN

Uncertain

0.61

MetaSVM

Benign

-0.72

MutationAssessor

Uncertain

2.9

PrimateAI

Uncertain

0.50

PROVEAN

Pathogenic

-5.9

REVEL

Benign

0.20

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.035

Polyphen

0.37

Vest4

0.47

MutPred

0.76

Gain of MoRF binding (P = 0.0301);

MVP

0.22

MPC

0.017

ClinPred

0.98

GERP RS

2.9

Varity_R

0.48

gMVP

0.62

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