chrX-49332772-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_001098412.4(GAGE13):āc.35C>Gā(p.Pro12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 4)
Exomes š: 0.0000052 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
GAGE13
NM_001098412.4 missense
NM_001098412.4 missense
Scores
1
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.461
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.08435115).
BP6
Variant X-49332772-C-G is Benign according to our data. Variant chrX-49332772-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3280466.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAGE13 | NM_001098412.4 | c.35C>G | p.Pro12Arg | missense_variant | 2/5 | ENST00000612958.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAGE13 | ENST00000612958.2 | c.35C>G | p.Pro12Arg | missense_variant | 2/5 | 1 | NM_001098412.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 4
GnomAD3 genomes
Cov.:
4
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000521 AC: 3AN: 575871Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0AN XY: 150663
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
575871
Hom.:
Cov.:
9
AF XY:
AC XY:
0
AN XY:
150663
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 4
GnomAD4 genome
Cov.:
4
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.