5-160238719-C-T

Variant summary

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

The ENST00000393980.8(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 ENST00000393980.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP6	NM_001040442.1	c.*60C>T		3_prime_UTR_variant	6/6
FABP6	NM_001445.3			downstream_gene_variant		ENST00000402432.4
FABP6	NM_001130958.2			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP6	ENST00000393980.8	c.*60C>T		3_prime_UTR_variant	7/7	1
FABP6	ENST00000402432.4			downstream_gene_variant		1	NM_001445.3	P1
FABP6	ENST00000521362.1			downstream_gene_variant		2
FABP6	ENST00000523955.5			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132987 AN: 151922 Hom.: 59051 Cov.: 33

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.: 20 AF XY: 0.934 AC XY: 646291 AN XY: 691934

Gnomad4 AFR exome AF: 0.699

Gnomad4 AMR exome AF: 0.941

Gnomad4 ASJ exome AF: 0.903

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.969

Gnomad4 FIN exome AF: 0.987

Gnomad4 NFE exome AF: 0.933

Gnomad4 OTH exome AF: 0.921

GnomAD4 genome AF: 0.875 AC: 133059 AN: 152040 Hom.: 59080 Cov.: 33 AF XY: 0.881 AC XY: 65522 AN XY: 74344

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.914

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.881

Alfa AF: 0.911 Hom.: 22248

Bravo AF: 0.861

Asia WGS AF: 0.959 AC: 3335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.20
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10071871; hg19: chr5-159665726;