Genetic Variant FABP6:c.*67C>T (chr5-160238726-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000393980.8(FABP6):c.*67C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 1,517,266 control chromosomes in the GnomAD database, including 566,843 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.77 ( 46589 hom., cov: 33)

Exomes 𝑓: 0.87 ( 520254 hom. )

Consequence

FABP6
ENST00000393980.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.89

Publications

4 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393980.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP6	NM_001445.3	MANE Select	c.*67C>T	downstream_gene	N/A	NP_001436.1	P51161-1
FABP6	NM_001040442.1		c.*67C>T	downstream_gene	N/A	NP_001035532.1	P51161-2
FABP6	NM_001130958.2		c.*67C>T	downstream_gene	N/A	NP_001124430.1	P51161-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FABP6	ENST00000393980.8	TSL:1	c.*67C>T	3_prime_UTR	Exon 7 of 7	ENSP00000377549.4	P51161-2
FABP6	ENST00000877317.1		c.*67C>T	3_prime_UTR	Exon 8 of 8	ENSP00000547376.1
FABP6	ENST00000877319.1		c.*67C>T	3_prime_UTR	Exon 8 of 8	ENSP00000547378.1

Frequencies

GnomAD3 genomes

AF:

0.766

AC:

116355

AN:

151910

Hom.:

46584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.907

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.836

Gnomad EAS

AF:

0.639

Gnomad SAS

AF:

0.841

Gnomad FIN

AF:

0.940

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.891

Gnomad OTH

AF:

0.764

GnomAD4 exome

AF:

0.869

AC:

1185965

AN:

1365238

Hom.:

520254

Cov.:

AF XY:

0.870

AC XY:

592015

AN XY:

680360

show subpopulations

African (AFR)

AF:

0.512

AC:

16164

AN:

31542

American (AMR)

AF:

0.690

AC:

30290

AN:

43896

Ashkenazi Jewish (ASJ)

AF:

0.830

AC:

21108

AN:

25432

East Asian (EAS)

AF:

0.621

AC:

24015

AN:

38700

South Asian (SAS)

AF:

0.858

AC:

71942

AN:

83892

European-Finnish (FIN)

AF:

0.935

AC:

49678

AN:

53122

Middle Eastern (MID)

AF:

0.752

AC:

4181

AN:

5558

European-Non Finnish (NFE)

AF:

0.897

AC:

920785

AN:

1026180

Other (OTH)

AF:

0.840

AC:

47802

AN:

56916

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

6705

13410

20114

26819

33524

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19376

38752

58128

77504

96880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.766

AC:

116396

AN:

152028

Hom.:

46589

Cov.:

AF XY:

0.767

AC XY:

57050

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.524

AC:

21686

AN:

41414

American (AMR)

AF:

0.741

AC:

11322

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.836

AC:

2897

AN:

3466

East Asian (EAS)

AF:

0.639

AC:

3292

AN:

5154

South Asian (SAS)

AF:

0.841

AC:

4049

AN:

4816

European-Finnish (FIN)

AF:

0.940

AC:

9975

AN:

10612

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.891

AC:

60541

AN:

67976

Other (OTH)

AF:

0.761

AC:

1602

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1228

2456

3683

4911

6139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.771

Hom.:

2936

Bravo

AF:

0.738

Asia WGS

AF:

0.722

AC:

2511

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.047

(source)

DANN

Benign

0.69

PhyloP100

-3.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over