16-81565999-C-T

Variant names:

• chr16-81565999-C-T
• rs2911278
• NM_198390.3:c.301-41568C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_198390.3(CMIP):​c.301-41568C>T 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 151,992 control chromosomes in the GnomAD database, including 12,794 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 (12794 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.301-41568C>T		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.301-41568C>T		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.19-41568C>T		intron_variant	Intron 1 of 20	1		ENSP00000440401.2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58049 AN: 151874 Hom.: 12788 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.382 AC: 58071 AN: 151992 Hom.: 12794 Cov.: 32 AF XY: 0.388 AC XY: 28783 AN XY: 74278

African (AFR) AF: 0.167 AC: 6913 AN: 41456

American (AMR) AF: 0.401 AC: 6139 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1018 AN: 5142

South Asian (SAS) AF: 0.489 AC: 2357 AN: 4818

European-Finnish (FIN) AF: 0.536 AC: 5657 AN: 10554

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33247 AN: 67948

Other (OTH) AF: 0.371 AC: 781 AN: 2106

Alfa AF: 0.393 Hom.: 2793

Bravo AF: 0.358

Asia WGS AF: 0.292 AC: 1020 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	0.26
DANN	Benign	0.81
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.43		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.43		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2911278; hg19: chr16-81599604;