16-81605585-C-T

Position:

• chr16-81605585-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.301-1982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,102 control chromosomes in the GnomAD database, including 8,635 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 0.33 (8635 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.301-1982C>T		intron_variant		ENST00000537098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.301-1982C>T		intron_variant		1	NM_198390.3	P1
CMIP	ENST00000539778.6	c.19-1982C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50720 AN: 151984 Hom.: 8619 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.334 AC: 50775 AN: 152102 Hom.: 8635 Cov.: 32 AF XY: 0.329 AC XY: 24491 AN XY: 74348

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.353

Alfa AF: 0.349 Hom.: 12625

Bravo AF: 0.339

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
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: rs7185203; hg19: chr16-81639190;