1-31372839-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004102.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP3	NM_004102.5	MANE Select	c.73+103G>C		intron	N/A	NP_004093.1
	FABP3	NM_001320996.2		c.73+103G>C		intron	N/A	NP_001307925.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FABP3	ENST00000373713.7	TSL:1 MANE Select	c.73+103G>C		intron	N/A	ENSP00000362817.2
	FABP3	ENST00000970076.1		c.73+103G>C		intron	N/A	ENSP00000640135.1
	FABP3	ENST00000915558.1		c.73+103G>C		intron	N/A	ENSP00000585617.1

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

African (AFR) AF: 0.103 AC: 2555 AN: 24830

American (AMR) AF: 0.0801 AC: 3366 AN: 42034

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 400 AN: 22372

East Asian (EAS) AF: 0.173 AC: 6407 AN: 37084

South Asian (SAS) AF: 0.203 AC: 15191 AN: 74908

European-Finnish (FIN) AF: 0.0562 AC: 2186 AN: 38878

Middle Eastern (MID) AF: 0.0319 AC: 156 AN: 4884

European-Non Finnish (NFE) AF: 0.0178 AC: 12798 AN: 719848

Other (OTH) AF: 0.0521 AC: 2389 AN: 45884

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

African (AFR) AF: 0.100 AC: 4171 AN: 41552

American (AMR) AF: 0.0567 AC: 867 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5170

South Asian (SAS) AF: 0.207 AC: 999 AN: 4826

European-Finnish (FIN) AF: 0.0613 AC: 651 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1300 AN: 68032

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.71
PhyloP100		-0.27
PromoterAI		-0.056	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2279885; hg19: chr1-31845686;