5-160227102-T-C

Variant names:

• chr5-160227102-T-C
• rs10041333
• ENST00000393980.8:c.136-2444T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt
FABP6	NM_001040442.1	c.136-2444T>C		intron_variant	Intron 2 of 5		NP_001035532.1
FABP6	NM_001130958.2	c.136-2444T>C		intron_variant	Intron 3 of 6		NP_001124430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP6	ENST00000393980.8	c.136-2444T>C		intron_variant	Intron 3 of 6	1		ENSP00000377549.4
FABP6	ENST00000523955.5	n.94-1371T>C		intron_variant	Intron 1 of 5	3		ENSP00000428766.1

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

African (AFR) AF: 0.445 AC: 18476 AN: 41494

American (AMR) AF: 0.272 AC: 4151 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3470

East Asian (EAS) AF: 0.0932 AC: 483 AN: 5184

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3365 AN: 10580

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25507 AN: 67992

Other (OTH) AF: 0.341 AC: 719 AN: 2106

Alfa AF: 0.368 Hom.: 17788

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
PhyloP100		-0.87
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: rs10041333; hg19: chr5-159654109;