rs12445748

Positions:

• chr16-81492032-T-C

Variant summary

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

The NM_198390.3(CMIP):​c.300+46491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0793 in 152,262 control chromosomes in the GnomAD database, including 643 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 0.079 (643 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+46491T>C		intron_variant		ENST00000537098.8
CMIP	XM_047434717.1	c.-3211T>C		5_prime_UTR_variant	2/22
CMIP	XM_011523352.2	c.300+46491T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+46491T>C		intron_variant		1	NM_198390.3	P1

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 12085 AN: 152144 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0793 AC: 12080 AN: 152262 Hom.: 643 Cov.: 32 AF XY: 0.0827 AC XY: 6154 AN XY: 74436

Gnomad4 AFR AF: 0.0183

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0923 Hom.: 1016

Bravo AF: 0.0723

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
DANN	Benign	0.67

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: rs12445748; hg19: chr16-81525637;