rs12934986

Positions:

• chr16-81519465-T-A
• chr16-81519465-T-C

Variant summary

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

The ENST00000537098.8(CMIP):​c.300+73924T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,288 control chromosomes in the GnomAD database, including 2,158 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 0.16 (2157 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1 hom.)
• Consequence: CMIP ENST00000537098.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+73924T>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.300+73924T>A		intron_variant		1	NM_198390.3	ENSP00000446100	P1
CMIP	ENST00000539778.6	c.18+23971T>A		intron_variant		1		ENSP00000440401
	ENST00000624318.1	n.1642T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24909 AN: 152088 Hom.: 2154 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.110 AC: 9 AN: 82 Hom.: 1 Cov.: 0 AF XY: 0.0606 AC XY: 4 AN XY: 66

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.167

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.164 AC: 24936 AN: 152206 Hom.: 2157 Cov.: 32 AF XY: 0.167 AC XY: 12463 AN XY: 74414

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.186

Alfa AF: 0.0846 Hom.: 109

Bravo AF: 0.164

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs12934986; hg19: chr16-81553070;