rs10914367

chr1-31373359-A-Gchr1-31373359-A-T

Variant summary

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

The ENST00000482018.1(FABP3):c.-27-318T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,274 control chromosomes in the GnomAD database, including 47,007 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 0.78 (47007 hom., cov: 34)
• Consequence: FABP3 ENST00000482018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FABP3	ENST00000482018.1	c.-27-318T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.782 AC: 119029 AN: 152156 Hom.: 46968 Cov.: 34

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.768

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.782 AC: 119120 AN: 152274 Hom.: 47007 Cov.: 34 AF XY: 0.776 AC XY: 57783 AN XY: 74448

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.768

Alfa AF: 0.785 Hom.: 77123

Bravo AF: 0.781

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.86
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10914367; hg19: chr1-31846206;