rs12523547

Variant names:

• chr5-160235717-G-C
• rs12523547
• NM_001445.3:c.333+808G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FABP6	NM_001445.3	c.333+808G>C		intron_variant	Intron 3 of 3	ENST00000402432.4	NP_001436.1
FABP6	NM_001040442.1	c.480+808G>C		intron_variant	Intron 5 of 5		NP_001035532.1
FABP6	NM_001130958.2	c.480+808G>C		intron_variant	Intron 6 of 6		NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000402432.4	c.333+808G>C		intron_variant	Intron 3 of 3	1	NM_001445.3	ENSP00000385433.4
FABP6	ENST00000393980.8	c.480+808G>C		intron_variant	Intron 6 of 6	1		ENSP00000377549.4
FABP6	ENST00000521362.1	n.329+808G>C		intron_variant	Intron 2 of 2	2
FABP6	ENST00000523955.5	n.*541+808G>C		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.466 AC: 19311 AN: 41458

American (AMR) AF: 0.441 AC: 6736 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3468

East Asian (EAS) AF: 0.568 AC: 2926 AN: 5150

South Asian (SAS) AF: 0.540 AC: 2602 AN: 4816

European-Finnish (FIN) AF: 0.497 AC: 5247 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27759 AN: 67954

Other (OTH) AF: 0.423 AC: 894 AN: 2114

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
PhyloP100		0.034
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12523547; hg19: chr5-159662724;