Variant chr5-160232266-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001445.3(FABP6):c.236C>T(p.Thr79Met) variant causes a missense change. The variant allele was found at a frequency of 0.419 in 1,602,626 control chromosomes in the GnomAD database, including 142,246 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.43 ( 14546 hom., cov: 30)

Exomes 𝑓: 0.42 ( 127700 hom. )

Consequence

FABP6
NM_001445.3 missense

Scores

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]

FABP6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.3707747E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FABP6	NM_001445.3 linkuse as main transcript	c.236C>T	p.Thr79Met	missense_variant	2/4	ENST00000402432.4
FABP6	NM_001040442.1 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	4/6
FABP6	NM_001130958.2 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP6	ENST00000402432.4 linkuse as main transcript	c.236C>T	p.Thr79Met	missense_variant	2/4	1	NM_001445.3	P1	P51161-1
FABP6	ENST00000393980.8 linkuse as main transcript	c.383C>T	p.Thr128Met	missense_variant	5/7	1			P51161-2
FABP6	ENST00000521362.1 linkuse as main transcript	n.232C>T		non_coding_transcript_exon_variant	1/3	2
FABP6	ENST00000523955.5 linkuse as main transcript	c.*444C>T		3_prime_UTR_variant, NMD_transcript_variant	4/6	3

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65898

AN:

151594

Hom.:

14532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.441

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.415

GnomAD3 exomes

AF:

0.443

AC:

104038

AN:

235094

Hom.:

23170

AF XY:

0.444

AC XY:

56241

AN XY:

126770

show subpopulations

Gnomad AFR exome

AF:

0.451

Gnomad AMR exome

AF:

0.473

Gnomad ASJ exome

AF:

0.410

Gnomad EAS exome

AF:

0.508

Gnomad SAS exome

AF:

0.532

Gnomad FIN exome

AF:

0.462

Gnomad NFE exome

AF:

0.396

Gnomad OTH exome

AF:

0.435

GnomAD4 exome

AF:

0.417

AC:

605556

AN:

1450912

Hom.:

127700

Cov.:

AF XY:

0.420

AC XY:

303116

AN XY:

720912

show subpopulations

Gnomad4 AFR exome

AF:

0.463

Gnomad4 AMR exome

AF:

0.466

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.530

Gnomad4 FIN exome

AF:

0.464

Gnomad4 NFE exome

AF:

0.402

Gnomad4 OTH exome

AF:

0.429

GnomAD4 genome

AF:

0.435

AC:

65954

AN:

151714

Hom.:

14546

Cov.:

AF XY:

0.439

AC XY:

32560

AN XY:

74100

show subpopulations

Gnomad4 AFR

AF:

0.454

Gnomad4 AMR

AF:

0.442

Gnomad4 ASJ

AF:

0.434

Gnomad4 EAS

AF:

0.508

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.483

Gnomad4 NFE

AF:

0.403

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.411

Hom.:

22450

Bravo

AF:

0.432

TwinsUK

AF:

0.403

AC:

1496

ALSPAC

AF:

0.398

AC:

1535

ESP6500AA

AF:

0.463

AC:

2042

ESP6500EA

AF:

0.400

AC:

3443

ExAC

AF:

0.431

AC:

52291

Asia WGS

AF:

0.524

AC:

1822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.047

.;T

Eigen

Benign

-0.45

Eigen_PC

Benign

-0.33

FATHMM_MKL

Benign

0.71

LIST_S2

Uncertain

0.92

D;D

MetaRNN

Benign

0.00024

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.34

.;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.080

N;N

REVEL

Benign

0.074

Sift

Benign

0.10

T;D

Sift4G

Uncertain

0.0080

D;D

Polyphen

0.26

B;B

Vest4

0.089

MPC

0.20

ClinPred

0.028

GERP RS

3.5

Varity_R

0.28

gMVP

0.49

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over