rs4265801

Positions:

• chr16-81631447-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.477+10521T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,126 control chromosomes in the GnomAD database, including 16,171 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 0.45 (16170 hom., cov: 33)
  • Exomes 𝑓: 0.63 (1 hom.)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

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]

ENSG00000279841 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMIP	NM_198390.3	c.477+10521T>G		intron_variant		ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.477+10521T>G		intron_variant		1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.195+10521T>G		intron_variant		1		ENSP00000440401.2
CMIP	ENST00000566513.5	c.-85+10521T>G		intron_variant		5		ENSP00000478272.1
ENSG00000279841	ENST00000624151.1	n.1255T>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68531 AN: 152000 Hom.: 16157 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.451 AC: 68575 AN: 152118 Hom.: 16170 Cov.: 33 AF XY: 0.447 AC XY: 33207 AN XY: 74346

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.458

Alfa AF: 0.503 Hom.: 9024

Bravo AF: 0.452

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
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: rs4265801; hg19: chr16-81665052;