rs13333580

Variant names:

• chr16-81454767-T-A
• rs13333580
• NM_198390.3:c.300+9226T>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+9226T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 152,190 control chromosomes in the GnomAD database, including 173 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 0.018 (173 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• 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]

ENSG00000297575 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+9226T>A		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2
CMIP	XM_011523352.2	c.300+9226T>A		intron_variant	Intron 1 of 19		XP_011521654.1
CMIP	XM_047434717.1	c.-16500+9226T>A		intron_variant	Intron 1 of 21		XP_047290673.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.300+9226T>A		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2
ENSG00000297575	ENST00000749040.1	n.144+7234T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2795 AN: 152072 Hom.: 173 Cov.: 33

Gnomad AFR AF: 0.00865

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00530

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.00699

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0184 AC: 2800 AN: 152190 Hom.: 173 Cov.: 33 AF XY: 0.0193 AC XY: 1438 AN XY: 74406

African (AFR) AF: 0.00868 AC: 360 AN: 41496

American (AMR) AF: 0.00530 AC: 81 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5168

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4824

European-Finnish (FIN) AF: 0.00699 AC: 74 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 796 AN: 68020

Other (OTH) AF: 0.0189 AC: 40 AN: 2116

Alfa AF: 0.0128 Hom.: 2

Bravo AF: 0.0190

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.86
PhyloP100		-0.25
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: rs13333580; hg19: chr16-81488372;