rs2271072

Positions:

• chr1-31367579-C-G

Variant summary

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

The NM_004102.5(FABP3):​c.247-85G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 1,123,366 control chromosomes in the GnomAD database, including 188,520 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 0.54 (23383 hom., cov: 32)
  • Exomes 𝑓: 0.57 (165137 hom.)
• Consequence: FABP3 NM_004102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

FABP3 (HGNC:3557): (fatty acid binding protein 3) The intracellular fatty acid-binding proteins (FABPs) belongs to a multigene family. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Fatty acid-binding protein 3 gene contains four exons and its function is to arrest growth of mammary epithelial cells. This gene is a candidate tumor suppressor gene for human breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP3	NM_004102.5	c.247-85G>C		intron_variant		ENST00000373713.7	NP_004093.1
FABP3	NM_001320996.2	c.280-85G>C		intron_variant			NP_001307925.1
FABP3	XM_011541007.4	c.247-85G>C		intron_variant			XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP3	ENST00000373713.7	c.247-85G>C		intron_variant		1	NM_004102.5	ENSP00000362817	P1
FABP3	ENST00000482018.1	c.247-85G>C		intron_variant		5		ENSP00000473982
FABP3	ENST00000498148.5	c.*44-85G>C		intron_variant, NMD_transcript_variant		2		ENSP00000474078
FABP3	ENST00000497275.5	n.207-85G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82650 AN: 151930 Hom.: 23384 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.558

GnomAD4 exome AF: 0.570 AC: 553916 AN: 971318 Hom.: 165137 AF XY: 0.565 AC XY: 284166 AN XY: 503210

Gnomad4 AFR exome AF: 0.461

Gnomad4 AMR exome AF: 0.502

Gnomad4 ASJ exome AF: 0.649

Gnomad4 EAS exome AF: 0.174

Gnomad4 SAS exome AF: 0.370

Gnomad4 FIN exome AF: 0.582

Gnomad4 NFE exome AF: 0.621

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.544 AC: 82656 AN: 152048 Hom.: 23383 Cov.: 32 AF XY: 0.535 AC XY: 39766 AN XY: 74342

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.554

Alfa AF: 0.593 Hom.: 3386

Bravo AF: 0.540

Asia WGS AF: 0.284 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.71

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: rs2271072; hg19: chr1-31840426; COSMIC: COSV60001540; COSMIC: COSV60001540;