rs16955379

chr16-81455768-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198390.3(CMIP):c.300+10227C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 152,198 control chromosomes in the GnomAD database, including 311 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 0.038 (311 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+10227C>T		intron_variant		ENST00000537098.8
CMIP	XM_011523352.2	c.300+10227C>T		intron_variant
CMIP	XM_047434717.1	c.-16500+10227C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+10227C>T		intron_variant		1	NM_198390.3	P1

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5704 AN: 152080 Hom.: 312 Cov.: 33

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00687

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0376 AC: 5718 AN: 152198 Hom.: 311 Cov.: 33 AF XY: 0.0375 AC XY: 2793 AN XY: 74410

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.0120

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.00687

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0218 Hom.: 120

Bravo AF: 0.0416

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.1
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs16955379; hg19: chr16-81489373;