ENST00000915558.1:c.-27-318T>C

Variant names:

• chr1-31373359-A-G
• rs10914367
• ENST00000915558.1:c.-27-318T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000915558.1(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 ENST00000915558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000915558.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP3	ENST00000915558.1		c.-27-318T>C		intron	N/A	ENSP00000585617.1
	FABP3	ENST00000482018.1	TSL:5	c.-27-318T>C		intron	N/A	ENSP00000473982.1

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

African (AFR) AF: 0.844 AC: 35082 AN: 41572

American (AMR) AF: 0.726 AC: 11115 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2543 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2800 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3008 AN: 4826

European-Finnish (FIN) AF: 0.773 AC: 8202 AN: 10606

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53797 AN: 68004

Other (OTH) AF: 0.768 AC: 1625 AN: 2116

Alfa AF: 0.786 Hom.: 129370

Bravo AF: 0.781

Asia WGS AF: 0.636 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.50
PhyloP100		-1.5
PromoterAI		0.064	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10914367; hg19: chr1-31846206;