rs4265801

Variant names:

• chr16-81631447-T-G
• rs4265801
• NM_198390.3:c.477+10521T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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]

ENSG00000279841 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198390.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMIP	NM_198390.3	MANE Select	c.477+10521T>G		intron	N/A	NP_938204.2	Q8IY22-1
	CMIP	NM_030629.3		c.195+10521T>G		intron	N/A	NP_085132.1	Q8IY22-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMIP	ENST00000537098.8	TSL:1 MANE Select	c.477+10521T>G		intron	N/A	ENSP00000446100.2	Q8IY22-1
	CMIP	ENST00000539778.6	TSL:1	c.195+10521T>G		intron	N/A	ENSP00000440401.2	Q8IY22-2
	CMIP	ENST00000566513.5	TSL:5	c.-85+10521T>G		intron	N/A	ENSP00000478272.1	A0A087WU05

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.327 AC: 13586 AN: 41518

American (AMR) AF: 0.469 AC: 7173 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1993 AN: 5168

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4826

European-Finnish (FIN) AF: 0.416 AC: 4392 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36204 AN: 67980

Other (OTH) AF: 0.458 AC: 964 AN: 2106

Alfa AF: 0.505 Hom.: 10222

Bravo AF: 0.452

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.67
PhyloP100		0.37
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: rs4265801; hg19: chr16-81665052;