16-81463297-G-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+17756G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 152,248 control chromosomes in the GnomAD database, including 207 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 0.021 (207 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+17756G>T		intron_variant		ENST00000537098.8
CMIP	XM_011523352.2	c.300+17756G>T		intron_variant
CMIP	XM_047434717.1	c.-16499-15447G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+17756G>T		intron_variant		1	NM_198390.3	P1

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3228 AN: 152128 Hom.: 207 Cov.: 33

Gnomad AFR AF: 0.00398

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00439

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0212 AC: 3230 AN: 152248 Hom.: 207 Cov.: 33 AF XY: 0.0239 AC XY: 1780 AN XY: 74428

Gnomad4 AFR AF: 0.00399

Gnomad4 AMR AF: 0.00438

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.0182

Gnomad4 FIN AF: 0.0506

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.00830 Hom.: 2

Bravo AF: 0.0187

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0090
Dann	Benign	0.61

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: rs12599890; hg19: chr16-81496902;