16-81562839-C-G

Position:

• chr16-81562839-C-G

Variant summary

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

The NM_198390.3(CMIP):​c.301-44728C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,104 control chromosomes in the GnomAD database, including 13,290 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 0.38 (13290 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

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 (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.301-44728C>G		intron_variant		ENST00000537098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.301-44728C>G		intron_variant		1	NM_198390.3	P1
CMIP	ENST00000539778.6	c.19-44728C>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58080 AN: 151986 Hom.: 13290 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.382 AC: 58077 AN: 152104 Hom.: 13290 Cov.: 33 AF XY: 0.387 AC XY: 28753 AN XY: 74334

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.373

Alfa AF: 0.445 Hom.: 2073

Bravo AF: 0.357

Asia WGS AF: 0.276 AC: 964 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	2.0
DANN	Benign	0.74

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: rs2966120; hg19: chr16-81596444;