Genetic Variant FABP6:c.*60C>T (chr5-160238719-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 NM_001040442.1(FABP6):c.*60C>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 0.927 in 1,538,618 control chromosomes in the GnomAD database, including 663,701 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 0.88 ( 59080 hom., cov: 33)

Exomes 𝑓: 0.93 ( 604621 hom. )

Consequence

FABP6
NM_001040442.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

5 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040442.1. 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_001040442.1		c.*60C>T	3_prime_UTR	Exon 6 of 6	NP_001035532.1	P51161-2
FABP6	NM_001445.3	MANE Select	c.*60C>T	downstream_gene	N/A	NP_001436.1	P51161-1
FABP6	NM_001130958.2		c.*60C>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.*60C>T	3_prime_UTR	Exon 7 of 7	ENSP00000377549.4	P51161-2
FABP6	ENST00000877317.1		c.*60C>T	3_prime_UTR	Exon 8 of 8	ENSP00000547376.1
FABP6	ENST00000877319.1		c.*60C>T	3_prime_UTR	Exon 8 of 8	ENSP00000547378.1

Frequencies

GnomAD3 genomes

AF:

0.875

AC:

132987

AN:

151922

Hom.:

59051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.910

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.973

Gnomad FIN

AF:

0.991

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.931

Gnomad OTH

AF:

0.880

GnomAD4 exome

AF:

0.933

AC:

1293312

AN:

1386578

Hom.:

604621

Cov.:

AF XY:

0.934

AC XY:

646291

AN XY:

691934

show subpopulations

African (AFR)

AF:

0.699

AC:

22360

AN:

32010

American (AMR)

AF:

0.941

AC:

41714

AN:

44350

Ashkenazi Jewish (ASJ)

AF:

0.903

AC:

23158

AN:

25644

East Asian (EAS)

AF:

1.00

AC:

38990

AN:

38994

South Asian (SAS)

AF:

0.969

AC:

81915

AN:

84518

European-Finnish (FIN)

AF:

0.987

AC:

52540

AN:

53250

Middle Eastern (MID)

AF:

0.866

AC:

4868

AN:

5624

European-Non Finnish (NFE)

AF:

0.933

AC:

974530

AN:

1044394

Other (OTH)

AF:

0.921

AC:

53237

AN:

57794

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3908

7816

11723

15631

19539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19944

39888

59832

79776

99720

<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:

0.875

AC:

133059

AN:

152040

Hom.:

59080

Cov.:

AF XY:

0.881

AC XY:

65522

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.709

AC:

29353

AN:

41396

American (AMR)

AF:

0.914

AC:

13973

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.908

AC:

3146

AN:

3464

East Asian (EAS)

AF:

1.00

AC:

5172

AN:

5174

South Asian (SAS)

AF:

0.973

AC:

4693

AN:

4822

European-Finnish (FIN)

AF:

0.991

AC:

10523

AN:

10616

Middle Eastern (MID)

AF:

0.813

AC:

239

AN:

294

European-Non Finnish (NFE)

AF:

0.931

AC:

63271

AN:

67972

Other (OTH)

AF:

0.881

AC:

1859

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

796

1592

2389

3185

3981

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.909

Hom.:

26920

Bravo

AF:

0.861

Asia WGS

AF:

0.959

AC:

3335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.20

(source)

DANN

Benign

0.51

PhyloP100

-1.2

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