chr4-119318976-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000134.4(FABP2):c.*65A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,262,452 control chromosomes in the GnomAD database, including 65,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.34 ( 8812 hom., cov: 31)
Exomes 𝑓: 0.31 ( 56230 hom. )
Consequence
FABP2
NM_000134.4 3_prime_UTR
NM_000134.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.735
Genes affected
FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 4-119318976-T-C is Benign according to our data. Variant chr4-119318976-T-C is described in ClinVar as [Benign]. Clinvar id is 1236503.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FABP2 | NM_000134.4 | c.*65A>G | 3_prime_UTR_variant | 4/4 | ENST00000274024.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FABP2 | ENST00000274024.4 | c.*65A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_000134.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.337 AC: 51158AN: 151636Hom.: 8795 Cov.: 31
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GnomAD4 exome AF: 0.313 AC: 347849AN: 1110700Hom.: 56230 Cov.: 14 AF XY: 0.309 AC XY: 175145AN XY: 566726
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GnomAD4 genome AF: 0.338 AC: 51219AN: 151752Hom.: 8812 Cov.: 31 AF XY: 0.335 AC XY: 24811AN XY: 74156
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at