Variant 8-81531265-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001105281.6(FABP12):c.51C>T(p.Ser17Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00299 in 1,606,768 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 19 hom. )

Consequence

FABP12
NM_001105281.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.426

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 8-81531265-G-A is Benign according to our data. Variant chr8-81531265-G-A is described in ClinVar as [Benign]. Clinvar id is 789297.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.426 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
FABP12	NM_001105281.6 linkuse as main transcript	c.51C>T	p.Ser17Ser	synonymous_variant	2/5	NP_001098751.1	A6NFH5
FABP12	XM_006716465.4 linkuse as main transcript	c.51C>T	p.Ser17Ser	synonymous_variant	2/5	XP_006716528.1	A6NFH5
FABP12	XM_011517577.3 linkuse as main transcript	c.51C>T	p.Ser17Ser	synonymous_variant	3/6	XP_011515879.1	A6NFH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
FABP12	ENST00000360464.6 linkuse as main transcript	c.51C>T	p.Ser17Ser	synonymous_variant	2/5	1	ENSP00000353650.4	A6NFH5
FABP12	ENST00000692030.1 linkuse as main transcript	c.51C>T	p.Ser17Ser	synonymous_variant	3/6		ENSP00000510293.1	A6NFH5
FABP12	ENST00000519696.1 linkuse as main transcript	n.3C>T		non_coding_transcript_exon_variant	1/4	5	ENSP00000427973.1	H0YAS1
ENSG00000253374	ENST00000523380.5 linkuse as main transcript	n.506-1657G>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00513

AC:

780

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00750

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.000567

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00178

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00356

AC:

849

AN:

238500

Hom.:

AF XY:

0.00379

AC XY:

488

AN XY:

128786

show subpopulations

Gnomad AFR exome

AF:

0.0130

Gnomad AMR exome

AF:

0.000749

Gnomad ASJ exome

AF:

0.00907

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.000379

Gnomad NFE exome

AF:

0.00161

Gnomad OTH exome

AF:

0.00359

GnomAD4 exome

AF:

0.00277

AC:

4024

AN:

1454588

Hom.:

Cov.:

AF XY:

0.00301

AC XY:

2172

AN XY:

722630

show subpopulations

Gnomad4 AFR exome

AF:

0.0129

Gnomad4 AMR exome

AF:

0.000751

Gnomad4 ASJ exome

AF:

0.00924

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0123

Gnomad4 FIN exome

AF:

0.000716

Gnomad4 NFE exome

AF:

0.00175

Gnomad4 OTH exome

AF:

0.00427

GnomAD4 genome

AF:

0.00515

AC:

784

AN:

152180

Hom.:

Cov.:

AF XY:

0.00511

AC XY:

380

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0129

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00750

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0125

Gnomad4 FIN

AF:

0.000567

Gnomad4 NFE

AF:

0.00178

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.00421

Hom.:

Bravo

AF:

0.00521

Asia WGS

AF:

0.00549

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 17, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

4.8

DANN

Benign

0.44

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