16-81643843-T-C

Variant names:

• chr16-81643843-T-C
• rs7201632
• NM_198390.3:c.478-8360T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 11 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]

LOC105371362 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
CMIP	NM_198390.3	c.478-8360T>C		intron_variant	Intron 3 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.478-8360T>C		intron_variant	Intron 3 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.196-8360T>C		intron_variant	Intron 3 of 20	1		ENSP00000440401.2
CMIP	ENST00000566513.5	c.-84-8360T>C		intron_variant	Intron 2 of 19	5		ENSP00000478272.1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53288 AN: 151816 Hom.: 11072 Cov.: 31

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

African (AFR) AF: 0.124 AC: 5153 AN: 41450

American (AMR) AF: 0.401 AC: 6118 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1956 AN: 5174

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4804

European-Finnish (FIN) AF: 0.374 AC: 3941 AN: 10550

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31442 AN: 67908

Other (OTH) AF: 0.385 AC: 815 AN: 2116

Alfa AF: 0.371 Hom.: 1962

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
PhyloP100		0.21
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs7201632; hg19: chr16-81677448;