rs9930117

chr16-81456352-A-Cchr16-81456352-A-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+10811A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,252 control chromosomes in the GnomAD database, including 433 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 0.051 (433 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+10811A>C		intron_variant		ENST00000537098.8
CMIP	XM_011523352.2	c.300+10811A>C		intron_variant
CMIP	XM_047434717.1	c.-16500+10811A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+10811A>C		intron_variant		1	NM_198390.3	P1

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7697 AN: 152134 Hom.: 431 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.00894

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0508 AC: 7727 AN: 152252 Hom.: 433 Cov.: 33 AF XY: 0.0505 AC XY: 3761 AN XY: 74430

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.00894

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0353 Hom.: 23

Bravo AF: 0.0562

Asia WGS AF: 0.109 AC: 380 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	0.90
Dann	Benign	0.42

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: rs9930117; hg19: chr16-81489957;