chr5-160228491-G-A

Position:

• chr5-160228491-G-A

Variant summary

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

The NM_001040442.1(FABP6):​c.136-1055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0563 in 456,246 control chromosomes in the GnomAD database, including 862 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 0.054 (246 hom., cov: 32)
  • Exomes 𝑓: 0.057 (616 hom.)
• Consequence: FABP6 NM_001040442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP6	NM_001040442.1	c.136-1055G>A		intron_variant			NP_001035532.1
FABP6	NM_001130958.2	c.136-1055G>A		intron_variant			NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8	c.136-1055G>A		intron_variant		1		ENSP00000377549.4
FABP6	ENST00000523955.5	n.112G>A		non_coding_transcript_exon_variant	2/6	3		ENSP00000428766.1

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8220 AN: 152168 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0497

GnomAD3 exomes AF: 0.0533 AC: 6839 AN: 128390 Hom.: 232 AF XY: 0.0557 AC XY: 3919 AN XY: 70318

Gnomad AFR exome AF: 0.0567

Gnomad AMR exome AF: 0.0320

Gnomad ASJ exome AF: 0.0845

Gnomad EAS exome AF: 0.000383

Gnomad SAS exome AF: 0.0778

Gnomad FIN exome AF: 0.0392

Gnomad NFE exome AF: 0.0600

Gnomad OTH exome AF: 0.0533

GnomAD4 exome AF: 0.0574 AC: 17440 AN: 303960 Hom.: 616 Cov.: 0 AF XY: 0.0596 AC XY: 10321 AN XY: 173072

Gnomad4 AFR exome AF: 0.0552

Gnomad4 AMR exome AF: 0.0315

Gnomad4 ASJ exome AF: 0.0857

Gnomad4 EAS exome AF: 0.000326

Gnomad4 SAS exome AF: 0.0771

Gnomad4 FIN exome AF: 0.0384

Gnomad4 NFE exome AF: 0.0578

Gnomad4 OTH exome AF: 0.0534

GnomAD4 genome AF: 0.0541 AC: 8239 AN: 152286 Hom.: 246 Cov.: 32 AF XY: 0.0536 AC XY: 3994 AN XY: 74470

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.0421

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0593 Hom.: 92

Bravo AF: 0.0518

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72812227; hg19: chr5-159655498;