ENST00000482018.1:c.-27-1531C>A

Variant names:

• chr1-31374572-G-T
• rs12401792
• ENST00000482018.1:c.-27-1531C>A

Variant summary

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

The ENST00000482018.1(FABP3):​c.-27-1531C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,194 control chromosomes in the GnomAD database, including 4,527 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 0.22 (4527 hom., cov: 32)
• Consequence: FABP3 ENST00000482018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 6 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]

LOC124903892 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482018.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP3	ENST00000482018.1	TSL:5	c.-27-1531C>A		intron	N/A	ENSP00000473982.1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34154 AN: 152076 Hom.: 4521 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.225 AC: 34172 AN: 152194 Hom.: 4527 Cov.: 32 AF XY: 0.230 AC XY: 17125 AN XY: 74390

African (AFR) AF: 0.103 AC: 4289 AN: 41540

American (AMR) AF: 0.286 AC: 4370 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 984 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2365 AN: 5168

South Asian (SAS) AF: 0.394 AC: 1904 AN: 4832

European-Finnish (FIN) AF: 0.260 AC: 2759 AN: 10594

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16669 AN: 67990

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.229 Hom.: 5278

Bravo AF: 0.221

Asia WGS AF: 0.372 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.48
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs12401792; hg19: chr1-31847419; COSMIC: COSV65500285;