Genetic Variant ENST00000393980.8:c.136-1055G>A (chr5-160228491-G-A) – 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.136-1055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0563 in 456,246 control chromosomes in the GnomAD database, including 862 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 0.054 ( 246 hom., cov: 32)

Exomes 𝑓: 0.057 ( 616 hom. )

Consequence

FABP6
ENST00000393980.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.163

Publications

0 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP6	NM_001040442.1 link	c.136-1055G>A		intron_variant	Intron 2 of 5		NP_001035532.1	P51161-2
FABP6	NM_001130958.2 link	c.136-1055G>A		intron_variant	Intron 3 of 6		NP_001124430.1	P51161-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8 link	c.136-1055G>A		intron_variant	Intron 3 of 6	1		ENSP00000377549.4		P51161-2
FABP6	ENST00000523955.5 link	n.112G>A		non_coding_transcript_exon_variant	Exon 2 of 6	3		ENSP00000428766.1		H0YB64

Frequencies

GnomAD3 genomes

AF:

0.0540

AC:

8220

AN:

152168

Hom.:

245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.0422

Gnomad ASJ

AF:

0.0793

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0718

Gnomad FIN

AF:

0.0413

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.0600

Gnomad OTH

AF:

0.0497

GnomAD2 exomes

AF:

0.0533

AC:

6839

AN:

128390

AF XY:

0.0557

show subpopulations

Gnomad AFR exome

AF:

0.0567

Gnomad AMR exome

AF:

0.0320

Gnomad ASJ exome

AF:

0.0845

Gnomad EAS exome

AF:

0.000383

Gnomad FIN exome

AF:

0.0392

Gnomad NFE exome

AF:

0.0600

Gnomad OTH exome

AF:

0.0533

GnomAD4 exome

AF:

0.0574

AC:

17440

AN:

303960

Hom.:

616

Cov.:

AF XY:

0.0596

AC XY:

10321

AN XY:

173072

show subpopulations

African (AFR)

AF:

0.0552

AC:

476

AN:

8626

American (AMR)

AF:

0.0315

AC:

859

AN:

27284

Ashkenazi Jewish (ASJ)

AF:

0.0857

AC:

925

AN:

10788

East Asian (EAS)

AF:

0.000326

AC:

AN:

9210

South Asian (SAS)

AF:

0.0771

AC:

4603

AN:

59740

European-Finnish (FIN)

AF:

0.0384

AC:

475

AN:

12364

Middle Eastern (MID)

AF:

0.0521

AC:

145

AN:

2782

European-Non Finnish (NFE)

AF:

0.0578

AC:

9194

AN:

158934

Other (OTH)

AF:

0.0534

AC:

760

AN:

14232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

1069

2137

3206

4274

5343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

204

272

340

<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:

0.0541

AC:

8239

AN:

152286

Hom.:

246

Cov.:

AF XY:

0.0536

AC XY:

3994

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0549

AC:

2282

AN:

41564

American (AMR)

AF:

0.0421

AC:

644

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0793

AC:

275

AN:

3468

East Asian (EAS)

AF:

0.00173

AC:

AN:

5188

South Asian (SAS)

AF:

0.0719

AC:

347

AN:

4826

European-Finnish (FIN)

AF:

0.0413

AC:

438

AN:

10614

Middle Eastern (MID)

AF:

0.0445

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0600

AC:

4079

AN:

68024

Other (OTH)

AF:

0.0539

AC:

114

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

401

801

1202

1602

2003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0573

Hom.:

121

Bravo

AF:

0.0518

Asia WGS

AF:

0.0460

AC:

162

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.2

(source)

DANN

Benign

0.47

PhyloP100

0.16

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over