10-47999714-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001137548.3(FAM25C):c.52G>A(p.Glu18Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 21)
Exomes 𝑓: 0.000060 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FAM25C
NM_001137548.3 missense
NM_001137548.3 missense
Scores
1
2
10
Clinical Significance
Conservation
PhyloP100: 1.75
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.12069708).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM25C | NM_001137548.3 | c.52G>A | p.Glu18Lys | missense_variant | 1/3 | ENST00000617224.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM25C | ENST00000617224.3 | c.52G>A | p.Glu18Lys | missense_variant | 1/3 | 1 | NM_001137548.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 10AN: 150444Hom.: 0 Cov.: 21 FAILED QC
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GnomAD3 exomes AF: 0.0000579 AC: 4AN: 69036Hom.: 0 AF XY: 0.0000290 AC XY: 1AN XY: 34490
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000596 AC: 83AN: 1391774Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 37AN XY: 686572
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000664 AC: 10AN: 150562Hom.: 0 Cov.: 21 AF XY: 0.0000544 AC XY: 4AN XY: 73470
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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 | Nov 29, 2023 | The c.52G>A (p.E18K) alteration is located in exon 1 (coding exon 1) of the FAM25C gene. This alteration results from a G to A substitution at nucleotide position 52, causing the glutamic acid (E) at amino acid position 18 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
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Uncertain
T
Sift4G
Pathogenic
D
Vest4
MVP
ClinPred
T
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