16-81503047-C-T

Position:

• chr16-81503047-C-T

Variant summary

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

The NM_198390.3(CMIP):​c.300+57506C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,126 control chromosomes in the GnomAD database, including 4,069 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 0.22 (4069 hom., cov: 33)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+57506C>T		intron_variant		ENST00000537098.8	NP_938204.2
CMIP	NM_030629.3	c.18+7553C>T		intron_variant			NP_085132.1
CMIP	XM_011523352.2	c.300+57506C>T		intron_variant			XP_011521654.1
CMIP	XM_047434717.1	c.252+7553C>T		intron_variant			XP_047290673.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.300+57506C>T		intron_variant		1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.18+7553C>T		intron_variant		1		ENSP00000440401.2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33258 AN: 152008 Hom.: 4063 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.219 AC: 33293 AN: 152126 Hom.: 4069 Cov.: 33 AF XY: 0.225 AC XY: 16727 AN XY: 74352

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.252

Alfa AF: 0.214 Hom.: 1977

Bravo AF: 0.215

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.66

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: rs4889327; hg19: chr16-81536652;