chr16-81620238-T-C

Variant names:

• chr16-81620238-T-C
• rs4074144
• NM_198390.3:c.427-638T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198390.3(CMIP):​c.427-638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,120 control chromosomes in the GnomAD database, including 16,318 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 (16312 hom., cov: 32)
  • Exomes 𝑓: 0.39 (6 hom.)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 4 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]

ENSG00000279294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.427-638T>C		intron_variant	Intron 2 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.427-638T>C		intron_variant	Intron 2 of 20	1	NM_198390.3	ENSP00000446100.2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67975 AN: 151924 Hom.: 16307 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.395 AC: 30 AN: 76 Hom.: 6 Cov.: 0 AF XY: 0.475 AC XY: 19 AN XY: 40

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.400 AC: 4 AN: 10

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: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.429 AC: 24 AN: 56

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.447 AC: 68012 AN: 152044 Hom.: 16312 Cov.: 32 AF XY: 0.444 AC XY: 32973 AN XY: 74296

African (AFR) AF: 0.288 AC: 11957 AN: 41476

American (AMR) AF: 0.537 AC: 8202 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2345 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1868 AN: 4804

European-Finnish (FIN) AF: 0.425 AC: 4494 AN: 10578

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35557 AN: 67974

Other (OTH) AF: 0.494 AC: 1040 AN: 2106

Alfa AF: 0.453 Hom.: 3128

Bravo AF: 0.454

Asia WGS AF: 0.383 AC: 1329 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	3.8
DANN	Benign	0.58
PhyloP100		-0.33
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: rs4074144; hg19: chr16-81653843;