5-160227102-T-C

Position:

• chr5-160227102-T-C

Variant summary

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

The ENST00000393980.8(FABP6):​c.136-2444T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,132 control chromosomes in the GnomAD database, including 10,676 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 0.37 (10676 hom., cov: 32)
• Consequence: FABP6 ENST00000393980.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP6	NM_001040442.1	c.136-2444T>C		intron_variant			NP_001035532.1
FABP6	NM_001130958.2	c.136-2444T>C		intron_variant			NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8	c.136-2444T>C		intron_variant		1		ENSP00000377549
FABP6	ENST00000523955.5	c.94-1371T>C		intron_variant, NMD_transcript_variant		3		ENSP00000428766

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55717 AN: 152014 Hom.: 10669 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.366 AC: 55753 AN: 152132 Hom.: 10676 Cov.: 32 AF XY: 0.359 AC XY: 26698 AN XY: 74372

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.0932

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.341

Alfa AF: 0.367 Hom.: 14096

Bravo AF: 0.363

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10041333; hg19: chr5-159654109;