NM_198390.3:c.300+70562C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198390.3(CMIP):​c.300+70562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,062 control chromosomes in the GnomAD database, including 41,901 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 41901 hom., cov: 31)

Consequence

CMIP
NM_198390.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.740

Publications

8 publications found
Variant links:
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CMIPNM_198390.3 linkc.300+70562C>T intron_variant Intron 1 of 20 ENST00000537098.8 NP_938204.2 Q8IY22-1
CMIPNM_030629.3 linkc.18+20609C>T intron_variant Intron 1 of 20 NP_085132.1 Q8IY22-2
CMIPXM_011523352.2 linkc.300+70562C>T intron_variant Intron 1 of 19 XP_011521654.1
CMIPXM_047434717.1 linkc.252+20609C>T intron_variant Intron 2 of 21 XP_047290673.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CMIPENST00000537098.8 linkc.300+70562C>T intron_variant Intron 1 of 20 1 NM_198390.3 ENSP00000446100.2 Q8IY22-1
CMIPENST00000539778.6 linkc.18+20609C>T intron_variant Intron 1 of 20 1 ENSP00000440401.2 Q8IY22-2

Frequencies

GnomAD3 genomes
AF:
0.734
AC:
111526
AN:
151942
Hom.:
41840
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.883
Gnomad AMI
AF:
0.682
Gnomad AMR
AF:
0.787
Gnomad ASJ
AF:
0.717
Gnomad EAS
AF:
0.840
Gnomad SAS
AF:
0.741
Gnomad FIN
AF:
0.570
Gnomad MID
AF:
0.658
Gnomad NFE
AF:
0.650
Gnomad OTH
AF:
0.726
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.734
AC:
111649
AN:
152062
Hom.:
41901
Cov.:
31
AF XY:
0.733
AC XY:
54480
AN XY:
74304
show subpopulations
African (AFR)
AF:
0.883
AC:
36664
AN:
41514
American (AMR)
AF:
0.788
AC:
12037
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.717
AC:
2485
AN:
3468
East Asian (EAS)
AF:
0.840
AC:
4332
AN:
5160
South Asian (SAS)
AF:
0.740
AC:
3562
AN:
4812
European-Finnish (FIN)
AF:
0.570
AC:
6021
AN:
10564
Middle Eastern (MID)
AF:
0.667
AC:
196
AN:
294
European-Non Finnish (NFE)
AF:
0.650
AC:
44197
AN:
67952
Other (OTH)
AF:
0.727
AC:
1534
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1461
2923
4384
5846
7307
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
836
1672
2508
3344
4180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.684
Hom.:
140581
Bravo
AF:
0.756
Asia WGS
AF:
0.771
AC:
2681
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.0
DANN
Benign
0.43
PhyloP100
-0.74
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.2
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2966097; hg19: chr16-81549708; API