chr1-31372839-C-G

Position:

• chr1-31372839-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.73+103G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 1,162,992 control chromosomes in the GnomAD database, including 3,483 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 0.061 (549 hom., cov: 32)
  • Exomes 𝑓: 0.045 (2934 hom.)
• Consequence: FABP3 NM_004102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FABP3	NM_004102.5	c.73+103G>C		intron_variant		ENST00000373713.7	NP_004093.1
FABP3	NM_001320996.2	c.73+103G>C		intron_variant			NP_001307925.1
FABP3	XM_011541007.4	c.73+103G>C		intron_variant			XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FABP3	ENST00000373713.7	c.73+103G>C		intron_variant		1	NM_004102.5	ENSP00000362817.2
FABP3	ENST00000482018.1	c.73+103G>C		intron_variant		5		ENSP00000473982.1
FABP3	ENST00000498148.5	n.73+103G>C		intron_variant		2		ENSP00000474078.1

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9227 AN: 152152 Hom.: 544 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0545

GnomAD4 exome AF: 0.0450 AC: 45448 AN: 1010722 Hom.: 2934 AF XY: 0.0503 AC XY: 26159 AN XY: 520228

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.0801

Gnomad4 ASJ exome AF: 0.0179

Gnomad4 EAS exome AF: 0.173

Gnomad4 SAS exome AF: 0.203

Gnomad4 FIN exome AF: 0.0562

Gnomad4 NFE exome AF: 0.0178

Gnomad4 OTH exome AF: 0.0521

GnomAD4 genome AF: 0.0608 AC: 9257 AN: 152270 Hom.: 549 Cov.: 32 AF XY: 0.0661 AC XY: 4920 AN XY: 74442

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0393 Hom.: 26

Bravo AF: 0.0609

Asia WGS AF: 0.236 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2279885; hg19: chr1-31845686;