16-81479031-T-G

Variant names:

• chr16-81479031-T-G
• rs1471152
• NM_198390.3:c.300+33490T>G

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+33490T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,062 control chromosomes in the GnomAD database, including 37,916 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 0.70 (37916 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 14 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+33490T>G		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2
CMIP	XM_047434717.1	c.-16212T>G		5_prime_UTR_variant	Exon 2 of 22		XP_047290673.1
CMIP	XM_011523352.2	c.300+33490T>G		intron_variant	Intron 1 of 19		XP_011521654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.300+33490T>G		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106127 AN: 151944 Hom.: 37864 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.699 AC: 106235 AN: 152062 Hom.: 37916 Cov.: 32 AF XY: 0.698 AC XY: 51871 AN XY: 74334

African (AFR) AF: 0.846 AC: 35101 AN: 41470

American (AMR) AF: 0.730 AC: 11157 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4048 AN: 5162

South Asian (SAS) AF: 0.637 AC: 3069 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6376 AN: 10574

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42221 AN: 67962

Other (OTH) AF: 0.678 AC: 1429 AN: 2108

Alfa AF: 0.644 Hom.: 134807

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.38
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1471152; hg19: chr16-81512636;