rs12523547

Positions:

• chr5-160235717-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001445.3(FABP6):​c.333+808G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,988 control chromosomes in the GnomAD database, including 15,232 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 0.44 (15232 hom., cov: 32)
• Consequence: FABP6 NM_001445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP6	NM_001445.3	c.333+808G>C		intron_variant		ENST00000402432.4	NP_001436.1
FABP6	NM_001040442.1	c.480+808G>C		intron_variant			NP_001035532.1
FABP6	NM_001130958.2	c.480+808G>C		intron_variant			NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000402432.4	c.333+808G>C		intron_variant		1	NM_001445.3	ENSP00000385433.4
FABP6	ENST00000393980.8	c.480+808G>C		intron_variant		1		ENSP00000377549.4
FABP6	ENST00000521362.1	n.329+808G>C		intron_variant		2
FABP6	ENST00000523955.5	n.*541+808G>C		intron_variant		3		ENSP00000428766.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67451 AN: 151870 Hom.: 15220 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.424

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.444 AC: 67500 AN: 151988 Hom.: 15232 Cov.: 32 AF XY: 0.450 AC XY: 33413 AN XY: 74282

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.423

Alfa AF: 0.432 Hom.: 1778

Bravo AF: 0.441

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.81

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

Other links and lift over

dbSNP: rs12523547; hg19: chr5-159662724;