chr1-31369306-C-T

Variant names:

• chr1-31369306-C-T
• rs11578034
• NM_004102.5:c.246+79G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004102.5(FABP3):​c.246+79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 1,478,564 control chromosomes in the GnomAD database, including 980 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 0.030 (79 hom., cov: 32)
  • Exomes 𝑓: 0.035 (901 hom.)
• Consequence: FABP3 NM_004102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

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=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4544/152242) while in subpopulation NFE AF= 0.0382 (2598/68000). AF 95% confidence interval is 0.037. There are 79 homozygotes in gnomad4. There are 2113 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP3	NM_004102.5	c.246+79G>A		intron_variant	Intron 2 of 3	ENST00000373713.7	NP_004093.1
FABP3	NM_001320996.2	c.279+79G>A		intron_variant	Intron 2 of 3		NP_001307925.1
FABP3	XM_011541007.4	c.246+79G>A		intron_variant	Intron 2 of 3		XP_011539309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP3	ENST00000373713.7	c.246+79G>A		intron_variant	Intron 2 of 3	1	NM_004102.5	ENSP00000362817.2
FABP3	ENST00000482018.1	c.246+79G>A		intron_variant	Intron 4 of 5	5		ENSP00000473982.1
FABP3	ENST00000497275.5	n.206+79G>A		intron_variant	Intron 1 of 2	2
FABP3	ENST00000498148.5	n.246+79G>A		intron_variant	Intron 2 of 4	2		ENSP00000474078.1

Frequencies

GnomAD3 genomes AF: 0.0299 AC: 4543 AN: 152124 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0363

GnomAD4 exome AF: 0.0347 AC: 45974 AN: 1326322 Hom.: 901 Cov.: 19 AF XY: 0.0344 AC XY: 22624 AN XY: 656868

Gnomad4 AFR exome AF: 0.0163

Gnomad4 AMR exome AF: 0.0187

Gnomad4 ASJ exome AF: 0.0758

Gnomad4 EAS exome AF: 0.0000258

Gnomad4 SAS exome AF: 0.0115

Gnomad4 FIN exome AF: 0.0401

Gnomad4 NFE exome AF: 0.0376

Gnomad4 OTH exome AF: 0.0352

GnomAD4 genome AF: 0.0298 AC: 4544 AN: 152242 Hom.: 79 Cov.: 32 AF XY: 0.0284 AC XY: 2113 AN XY: 74458

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0382

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.0368 Hom.: 135

Bravo AF: 0.0289

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11578034; hg19: chr1-31842153;