chr16-81519465-T-A

Variant names:

• chr16-81519465-T-A
• rs12934986
• NM_198390.3:c.300+73924T>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.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 NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 3 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]

ENSG00000279476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198390.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMIP	NM_198390.3	MANE Select	c.300+73924T>A		intron	N/A	NP_938204.2
	CMIP	NM_030629.3		c.18+23971T>A		intron	N/A	NP_085132.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMIP	ENST00000537098.8	TSL:1 MANE Select	c.300+73924T>A		intron	N/A	ENSP00000446100.2
	CMIP	ENST00000539778.6	TSL:1	c.18+23971T>A		intron	N/A	ENSP00000440401.2
	ENSG00000279476	ENST00000624318.1	TSL:6	n.1642T>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.167 AC: 1 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.114 AC: 8 AN: 70

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.146 AC: 6055 AN: 41538

American (AMR) AF: 0.205 AC: 3137 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1369 AN: 5176

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10590

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10516 AN: 67998

Other (OTH) AF: 0.186 AC: 393 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.81
PhyloP100		0.18
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs12934986; hg19: chr16-81553070;