5-160238726-C-T

Position:

• chr5-160238726-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.89

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.160238726C>T		intergenic_region
FABP6	NM_001445.3	c.*67C>T		downstream_gene_variant		ENST00000402432.4	NP_001436.1
FABP6	NM_001040442.1	c.*67C>T		downstream_gene_variant			NP_001035532.1
FABP6	NM_001130958.2	c.*67C>T		downstream_gene_variant			NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8	c.*67C>T		3_prime_UTR_variant	7/7	1		ENSP00000377549.4
FABP6	ENST00000402432.4	c.*67C>T		downstream_gene_variant		1	NM_001445.3	ENSP00000385433.4
FABP6	ENST00000521362.1	n.*10C>T		downstream_gene_variant		2
FABP6	ENST00000523955.5	n.*662C>T		downstream_gene_variant		3		ENSP00000428766.1

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116355 AN: 151910 Hom.: 46584 Cov.: 33

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.: 19 AF XY: 0.870 AC XY: 592015 AN XY: 680360

Gnomad4 AFR exome AF: 0.512

Gnomad4 AMR exome AF: 0.690

Gnomad4 ASJ exome AF: 0.830

Gnomad4 EAS exome AF: 0.621

Gnomad4 SAS exome AF: 0.858

Gnomad4 FIN exome AF: 0.935

Gnomad4 NFE exome AF: 0.897

Gnomad4 OTH exome AF: 0.840

GnomAD4 genome AF: 0.766 AC: 116396 AN: 152028 Hom.: 46589 Cov.: 33 AF XY: 0.767 AC XY: 57050 AN XY: 74334

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.940

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.761

Alfa AF: 0.795 Hom.: 2824

Bravo AF: 0.738

Asia WGS AF: 0.722 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.047
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2277953; hg19: chr5-159665733; COSMIC: COSV67436761; COSMIC: COSV67436761;