1-31372839-C-A

Variant names:

• chr1-31372839-C-A
• rs2279885
• NM_004102.5:c.73+103G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004102.5(FABP3):​c.73+103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000989 in 1,011,018 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 9.9e-7 (0 hom.)
• Consequence: FABP3 NM_004102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP3	NM_004102.5	c.73+103G>T		intron_variant	Intron 1 of 3	ENST00000373713.7	NP_004093.1
FABP3	NM_001320996.2	c.73+103G>T		intron_variant	Intron 1 of 3		NP_001307925.1
FABP3	XM_011541007.4	c.73+103G>T		intron_variant	Intron 1 of 3		XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP3	ENST00000373713.7	c.73+103G>T		intron_variant	Intron 1 of 3	1	NM_004102.5	ENSP00000362817.2
FABP3	ENST00000482018.1	c.73+103G>T		intron_variant	Intron 3 of 5	5		ENSP00000473982.1
FABP3	ENST00000498148.5	n.73+103G>T		intron_variant	Intron 1 of 4	2		ENSP00000474078.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 9.89e-7 AC: 1 AN: 1011018 Hom.: 0 AF XY: 0.00000192 AC XY: 1 AN XY: 520376

African (AFR) AF: 0.00 AC: 0 AN: 24854

American (AMR) AF: 0.00 AC: 0 AN: 42052

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22372

East Asian (EAS) AF: 0.00 AC: 0 AN: 37106

South Asian (SAS) AF: 0.00 AC: 0 AN: 74966

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38888

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4886

European-Non Finnish (NFE) AF: 0.00000139 AC: 1 AN: 719992

Other (OTH) AF: 0.00 AC: 0 AN: 45902

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		-0.27
PromoterAI		-0.027	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2279885; hg19: chr1-31845686;