rs11578034
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
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
NM_004102.5 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 79 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FABP3 | NM_004102.5 | c.246+79G>A | intron_variant | ENST00000373713.7 | |||
FABP3 | NM_001320996.2 | c.279+79G>A | intron_variant | ||||
FABP3 | XM_011541007.4 | c.246+79G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FABP3 | ENST00000373713.7 | c.246+79G>A | intron_variant | 1 | NM_004102.5 | P1 | |||
FABP3 | ENST00000482018.1 | c.246+79G>A | intron_variant | 5 | |||||
FABP3 | ENST00000498148.5 | c.246+79G>A | intron_variant, NMD_transcript_variant | 2 | |||||
FABP3 | ENST00000497275.5 | n.206+79G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0299 AC: 4543AN: 152124Hom.: 79 Cov.: 32
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GnomAD4 exome AF: 0.0347 AC: 45974AN: 1326322Hom.: 901 Cov.: 19 AF XY: 0.0344 AC XY: 22624AN XY: 656868
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GnomAD4 genome ? AF: 0.0298 AC: 4544AN: 152242Hom.: 79 Cov.: 32 AF XY: 0.0284 AC XY: 2113AN XY: 74458
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at