16-81479031-T-G

Position:

• chr16-81479031-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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/exons	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+33490T>G		intron_variant		ENST00000537098.8	NP_938204.2
CMIP	XM_047434717.1	c.-16212T>G		5_prime_UTR_variant	2/22		XP_047290673.1
CMIP	XM_011523352.2	c.300+33490T>G		intron_variant			XP_011521654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.300+33490T>G		intron_variant		1	NM_198390.3	ENSP00000446100	P1

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

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.678

Alfa AF: 0.630 Hom.: 58968

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1471152; hg19: chr16-81512636;