16-81445260-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198390.3(CMIP):c.19T>G(p.Ser7Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,514,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000050 ( 0 hom. )
Consequence
CMIP
NM_198390.3 missense
NM_198390.3 missense
Scores
2
1
16
Clinical Significance
Conservation
PhyloP100: 2.86
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=0.030059844).
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CMIP | NM_198390.3 | c.19T>G | p.Ser7Ala | missense_variant | 1/21 | ENST00000537098.8 | |
CMIP | XM_011523352.2 | c.19T>G | p.Ser7Ala | missense_variant | 1/20 | ||
CMIP | XM_047434717.1 | c.-16781T>G | 5_prime_UTR_variant | 1/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CMIP | ENST00000537098.8 | c.19T>G | p.Ser7Ala | missense_variant | 1/21 | 1 | NM_198390.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000405 AC: 6AN: 148184Hom.: 0 Cov.: 30
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?
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GnomAD3 exomes AF: 0.0000803 AC: 11AN: 137006Hom.: 0 AF XY: 0.0000940 AC XY: 7AN XY: 74476
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GnomAD4 exome AF: 0.0000498 AC: 68AN: 1366462Hom.: 0 Cov.: 35 AF XY: 0.0000579 AC XY: 39AN XY: 673790
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GnomAD4 genome ? AF: 0.0000405 AC: 6AN: 148184Hom.: 0 Cov.: 30 AF XY: 0.0000277 AC XY: 2AN XY: 72222
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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 | Feb 06, 2023 | The c.19T>G (p.S7A) alteration is located in exon 1 (coding exon 1) of the CMIP gene. This alteration results from a T to G substitution at nucleotide position 19, causing the serine (S) at amino acid position 7 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
Uncertain
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
Pathogenic
D
Polyphen
B
Vest4
MutPred
Loss of glycosylation at S7 (P = 0.0062);
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