chr1-121183396-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001100910.2(FAM72B):āc.94G>Cā(p.Ala32Pro) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000018 ( 0 hom., cov: 13)
Exomes š: 0.000013 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FAM72B
NM_001100910.2 missense
NM_001100910.2 missense
Scores
6
6
4
Clinical Significance
Conservation
PhyloP100: 6.99
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.786
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM72B | NM_001100910.2 | c.94G>C | p.Ala32Pro | missense_variant | 1/4 | ENST00000369390.7 | |
FAM72B | NM_001320149.2 | c.32+62G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM72B | ENST00000369390.7 | c.94G>C | p.Ala32Pro | missense_variant | 1/4 | 1 | NM_001100910.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 109858Hom.: 0 Cov.: 13 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000135 AC: 19AN: 1409044Hom.: 0 Cov.: 24 AF XY: 0.0000186 AC XY: 13AN XY: 699700
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000182 AC: 2AN: 109858Hom.: 0 Cov.: 13 AF XY: 0.0000193 AC XY: 1AN XY: 51700
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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 | Aug 08, 2023 | The c.94G>C (p.A32P) alteration is located in exon 1 (coding exon 1) of the FAM72B gene. This alteration results from a G to C substitution at nucleotide position 94, causing the alanine (A) at amino acid position 32 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;.;D
Sift
Uncertain
D;.;D
Sift4G
Pathogenic
D;D;D
Vest4
MutPred
Loss of sheet (P = 0.0181);Loss of sheet (P = 0.0181);.;
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at