rs2012502

Variant names:

• chr16-81694476-C-A
• rs2012502
• NM_198390.3:c.1530+989C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198390.3(CMIP):​c.1530+989C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,942 control chromosomes in the GnomAD database, including 11,473 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 (11473 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 11 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.1530+989C>A		intron_variant	Intron 13 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.1530+989C>A		intron_variant	Intron 13 of 20	1	NM_198390.3	ENSP00000446100.2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57414 AN: 151824 Hom.: 11456 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.378 AC: 57482 AN: 151942 Hom.: 11473 Cov.: 32 AF XY: 0.372 AC XY: 27658 AN XY: 74278

African (AFR) AF: 0.482 AC: 19973 AN: 41408

American (AMR) AF: 0.307 AC: 4695 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.168 AC: 866 AN: 5168

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4810

European-Finnish (FIN) AF: 0.348 AC: 3666 AN: 10546

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25022 AN: 67952

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.366 Hom.: 40560

Bravo AF: 0.379

Asia WGS AF: 0.194 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2012502; hg19: chr16-81728081;