chr1-121183405-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001100910.2(FAM72B):c.85G>A(p.Gly29Arg) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., cov: 13)
Exomes 𝑓: 0.000024 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FAM72B
NM_001100910.2 missense
NM_001100910.2 missense
Scores
5
8
3
Clinical Significance
Conservation
PhyloP100: 6.99
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.847
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM72B | NM_001100910.2 | c.85G>A | p.Gly29Arg | missense_variant | 1/4 | ENST00000369390.7 | |
FAM72B | NM_001320149.2 | c.32+53G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM72B | ENST00000369390.7 | c.85G>A | p.Gly29Arg | missense_variant | 1/4 | 1 | NM_001100910.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 110826Hom.: 0 Cov.: 13 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000238 AC: 34AN: 1427076Hom.: 0 Cov.: 26 AF XY: 0.0000254 AC XY: 18AN XY: 708980
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000180 AC: 2AN: 110826Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 52154
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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 | Oct 20, 2021 | The c.85G>A (p.G29R) alteration is located in exon 1 (coding exon 1) of the FAM72B gene. This alteration results from a G to A substitution at nucleotide position 85, causing the glycine (G) at amino acid position 29 to be replaced by an arginine (R). 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
Uncertain
CADD
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.
Sift
Uncertain
D;.
Sift4G
Uncertain
D;D
Vest4
MutPred
Loss of sheet (P = 0.0037);Loss of sheet (P = 0.0037);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at