chr16-81445321-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198390.3(CMIP):c.80T>C(p.Val27Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,581,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000035 ( 0 hom. )
Consequence
CMIP
NM_198390.3 missense
NM_198390.3 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 1.93
Genes affected
CMIP (HGNC:24319): (c-Maf inducing protein) This gene encodes a c-Maf inducing protein that plays a role in T-cell signaling pathway. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.021051258).
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMIP | NM_198390.3 | c.80T>C | p.Val27Ala | missense_variant | 1/21 | ENST00000537098.8 | |
CMIP | XM_011523352.2 | c.80T>C | p.Val27Ala | missense_variant | 1/20 | ||
CMIP | XM_047434717.1 | c.-16720T>C | 5_prime_UTR_variant | 1/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMIP | ENST00000537098.8 | c.80T>C | p.Val27Ala | missense_variant | 1/21 | 1 | NM_198390.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000462 AC: 7AN: 151538Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000827 AC: 16AN: 193586Hom.: 0 AF XY: 0.0000758 AC XY: 8AN XY: 105524
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GnomAD4 exome AF: 0.0000350 AC: 50AN: 1430058Hom.: 0 Cov.: 35 AF XY: 0.0000325 AC XY: 23AN XY: 708622
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GnomAD4 genome ? AF: 0.0000462 AC: 7AN: 151650Hom.: 0 Cov.: 30 AF XY: 0.0000405 AC XY: 3AN XY: 74130
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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 22, 2021 | The c.80T>C (p.V27A) alteration is located in exon 1 (coding exon 1) of the CMIP gene. This alteration results from a T to C substitution at nucleotide position 80, causing the valine (V) at amino acid position 27 to be replaced by an alanine (A). 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
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of glycosylation at S28 (P = 0.1526);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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