chr5-160228491-G-A

Variant names:

• chr5-160228491-G-A
• rs72812227
• ENST00000393980.8:c.136-1055G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040442.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP6	NM_001040442.1		c.136-1055G>A		intron	N/A	NP_001035532.1
	FABP6	NM_001130958.2		c.136-1055G>A		intron	N/A	NP_001124430.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP6	ENST00000393980.8	TSL:1	c.136-1055G>A		intron	N/A	ENSP00000377549.4
	FABP6	ENST00000877319.1		c.-214G>A		5_prime_UTR	Exon 4 of 8	ENSP00000547378.1
	FABP6	ENST00000968086.1		c.-214G>A		5_prime_UTR	Exon 2 of 6	ENSP00000638145.1

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

GnomAD2 exomes AF: 0.0533 AC: 6839 AN: 128390 AF XY: 0.0557

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 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

African (AFR) AF: 0.0552 AC: 476 AN: 8626

American (AMR) AF: 0.0315 AC: 859 AN: 27284

Ashkenazi Jewish (ASJ) AF: 0.0857 AC: 925 AN: 10788

East Asian (EAS) AF: 0.000326 AC: 3 AN: 9210

South Asian (SAS) AF: 0.0771 AC: 4603 AN: 59740

European-Finnish (FIN) AF: 0.0384 AC: 475 AN: 12364

Middle Eastern (MID) AF: 0.0521 AC: 145 AN: 2782

European-Non Finnish (NFE) AF: 0.0578 AC: 9194 AN: 158934

Other (OTH) AF: 0.0534 AC: 760 AN: 14232

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

African (AFR) AF: 0.0549 AC: 2282 AN: 41564

American (AMR) AF: 0.0421 AC: 644 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3468

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5188

South Asian (SAS) AF: 0.0719 AC: 347 AN: 4826

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10614

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0600 AC: 4079 AN: 68024

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0573 Hom.: 121

Bravo AF: 0.0518

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		0.16
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: rs72812227; hg19: chr5-159655498;