16-81643843-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198390.3(CMIP):​c.478-8360T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,936 control chromosomes in the GnomAD database, including 11,077 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 0.35 ( 11077 hom., cov: 31)

Consequence

CMIP
NM_198390.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.207
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CMIPNM_198390.3 linkc.478-8360T>C intron_variant Intron 3 of 20 ENST00000537098.8 NP_938204.2 Q8IY22-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CMIPENST00000537098.8 linkc.478-8360T>C intron_variant Intron 3 of 20 1 NM_198390.3 ENSP00000446100.2 Q8IY22-1
CMIPENST00000539778.6 linkc.196-8360T>C intron_variant Intron 3 of 20 1 ENSP00000440401.2 Q8IY22-2
CMIPENST00000566513.5 linkc.-84-8360T>C intron_variant Intron 2 of 19 5 ENSP00000478272.1 A0A087WU05

Frequencies

GnomAD3 genomes
AF:
0.351
AC:
53288
AN:
151816
Hom.:
11072
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.483
Gnomad AMR
AF:
0.401
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.378
Gnomad SAS
AF:
0.365
Gnomad FIN
AF:
0.374
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.463
Gnomad OTH
AF:
0.383
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.351
AC:
53302
AN:
151936
Hom.:
11077
Cov.:
31
AF XY:
0.351
AC XY:
26032
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.378
Gnomad4 SAS
AF:
0.366
Gnomad4 FIN
AF:
0.374
Gnomad4 NFE
AF:
0.463
Gnomad4 OTH
AF:
0.385
Alfa
AF:
0.378
Hom.:
1956
Bravo
AF:
0.344
Asia WGS
AF:
0.306
AC:
1066
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
4.4
DANN
Benign
0.42
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7201632; hg19: chr16-81677448; API