16-81501185-T-C

Variant summary

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

The NM_198390.3(CMIP):c.300+55644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,196 control chromosomes in the GnomAD database, including 38,057 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 0.71 (38057 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+55644T>C		intron_variant		ENST00000537098.8
CMIP	NM_030629.3	c.18+5691T>C		intron_variant
CMIP	XM_011523352.2	c.300+55644T>C		intron_variant
CMIP	XM_047434717.1	c.252+5691T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+55644T>C		intron_variant		1	NM_198390.3	P1
CMIP	ENST00000539778.6	c.18+5691T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107405 AN: 152078 Hom.: 38028 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.706 AC: 107495 AN: 152196 Hom.: 38057 Cov.: 33 AF XY: 0.706 AC XY: 52553 AN XY: 74408

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.713

Alfa AF: 0.707 Hom.: 69874

Bravo AF: 0.712

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.51
Dann	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2925979; hg19: chr16-81534790;