16-81656486-C-T

Variant names:

• chr16-81656486-C-T
• rs4243209
• NM_198390.3:c.640-1289C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198390.3(CMIP):​c.640-1289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,106 control chromosomes in the GnomAD database, including 41,783 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 (41783 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.640-1289C>T		intron_variant	Intron 4 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.640-1289C>T		intron_variant	Intron 4 of 20	1	NM_198390.3	ENSP00000446100.2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111318 AN: 151986 Hom.: 41754 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.766

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.732 AC: 111403 AN: 152106 Hom.: 41783 Cov.: 33 AF XY: 0.726 AC XY: 53991 AN XY: 74368

African (AFR) AF: 0.579 AC: 24002 AN: 41450

American (AMR) AF: 0.763 AC: 11668 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2772 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2692 AN: 5180

South Asian (SAS) AF: 0.695 AC: 3353 AN: 4822

European-Finnish (FIN) AF: 0.731 AC: 7731 AN: 10572

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56619 AN: 68004

Other (OTH) AF: 0.758 AC: 1601 AN: 2112

Alfa AF: 0.806 Hom.: 82613

Bravo AF: 0.727

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		-0.78
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

Other links and lift over

dbSNP: rs4243209; hg19: chr16-81690091;