rs2012502

Positions:

• chr16-81694476-C-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	Protein	UniProt
CMIP	NM_198390.3	c.1530+989C>A		intron_variant		ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.1530+989C>A		intron_variant		1	NM_198390.3	ENSP00000446100	P1

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.373

Alfa AF: 0.359 Hom.: 17041

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

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: rs2012502; hg19: chr16-81728081;