5-160238726-C-T

Variant names:

• chr5-160238726-C-T
• rs2277953
• ENST00000393980.8:c.*67C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.82).
• 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 rank	MANE	Protein	UniProt
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 rank	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8	c.*67C>T		3_prime_UTR_variant	Exon 7 of 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

African (AFR) AF: 0.512 AC: 16164 AN: 31542

American (AMR) AF: 0.690 AC: 30290 AN: 43896

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 21108 AN: 25432

East Asian (EAS) AF: 0.621 AC: 24015 AN: 38700

South Asian (SAS) AF: 0.858 AC: 71942 AN: 83892

European-Finnish (FIN) AF: 0.935 AC: 49678 AN: 53122

Middle Eastern (MID) AF: 0.752 AC: 4181 AN: 5558

European-Non Finnish (NFE) AF: 0.897 AC: 920785 AN: 1026180

Other (OTH) AF: 0.840 AC: 47802 AN: 56916

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

African (AFR) AF: 0.524 AC: 21686 AN: 41414

American (AMR) AF: 0.741 AC: 11322 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2897 AN: 3466

East Asian (EAS) AF: 0.639 AC: 3292 AN: 5154

South Asian (SAS) AF: 0.841 AC: 4049 AN: 4816

European-Finnish (FIN) AF: 0.940 AC: 9975 AN: 10612

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60541 AN: 67976

Other (OTH) AF: 0.761 AC: 1602 AN: 2104

Alfa AF: 0.771 Hom.: 2936

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
PhyloP100		-3.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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