rs1545224

chr2-88124297-A-G

Variant summary

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

The NM_001443.3(FABP1):c.333+197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 518,684 control chromosomes in the GnomAD database, including 16,974 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 0.19 (3532 hom., cov: 32)
  • Exomes 𝑓: 0.25 (13442 hom.)
• Consequence: FABP1 NM_001443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

FABP1 (HGNC:3555): (fatty acid binding protein 1) This gene encodes the fatty acid binding protein found in liver. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. This protein and FABP6 (the ileal fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FABP1	NM_001443.3	c.333+197T>C		intron_variant		ENST00000295834.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP1	ENST00000295834.8	c.333+197T>C		intron_variant		1	NM_001443.3	P1
FABP1	ENST00000393750.3	c.*155T>C		3_prime_UTR_variant	3/3	2
FABP1	ENST00000495375.1	n.816T>C		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28989 AN: 151984 Hom.: 3529 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.248 AC: 90900 AN: 366582 Hom.: 13442 Cov.: 4 AF XY: 0.257 AC XY: 49117 AN XY: 190820

Gnomad4 AFR exome AF: 0.0949

Gnomad4 AMR exome AF: 0.147

Gnomad4 ASJ exome AF: 0.208

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.466

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.228

GnomAD4 genome AF: 0.191 AC: 28992 AN: 152102 Hom.: 3532 Cov.: 32 AF XY: 0.194 AC XY: 14464 AN XY: 74370

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.200

Alfa AF: 0.223 Hom.: 8390

Bravo AF: 0.184

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.7
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545224; hg19: chr2-88423816; COSMIC: COSV55559081; COSMIC: COSV55559081;