6-122780422-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001446.5(FABP7):c.205G>A(p.Glu69Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,598 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
FABP7
NM_001446.5 missense
NM_001446.5 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 6.76
Genes affected
FABP7 (HGNC:3562): (fatty acid binding protein 7) The gene encodes a small, highly conserved cytoplasmic protein that bind long-chain fatty acids and other hydrophobic ligands. The encoded protein is important in the establishment of the radial glial fiber in the developing brain. Alternative splicing and promoter usage results in multiple transcript variants encoding different isoforms. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FABP7 | NM_001446.5 | c.205G>A | p.Glu69Lys | missense_variant | 2/4 | ENST00000368444.8 | NP_001437.1 | |
FABP7 | NM_001319039.2 | c.205G>A | p.Glu69Lys | missense_variant | 2/3 | NP_001305968.1 | ||
FABP7 | NM_001319042.2 | c.193G>A | p.Glu65Lys | missense_variant | 2/4 | NP_001305971.1 | ||
FABP7 | NM_001319041.2 | c.205G>A | p.Glu69Lys | missense_variant | 2/2 | NP_001305970.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250846Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135554
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461598Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727062
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GnomAD4 genome Cov.: 33
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33
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.205G>A (p.E69K) alteration is located in exon 2 (coding exon 2) of the FABP7 gene. This alteration results from a G to A substitution at nucleotide position 205, causing the glutamic acid (E) at amino acid position 69 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;T
Sift4G
Uncertain
D;T
Polyphen
B;.
Vest4
MutPred
Gain of ubiquitination at E69 (P = 0.0177);Gain of ubiquitination at E69 (P = 0.0177);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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