16-81627962-G-C

Variant names:

• chr16-81627962-G-C
• rs3935802
• NM_198390.3:c.477+7036G>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.477+7036G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,956 control chromosomes in the GnomAD database, including 12,640 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 0.40 (12640 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 7 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.477+7036G>C		intron_variant	Intron 3 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.477+7036G>C		intron_variant	Intron 3 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.195+7036G>C		intron_variant	Intron 3 of 20	1		ENSP00000440401.2
CMIP	ENST00000566513.5	c.-85+7036G>C		intron_variant	Intron 2 of 19	5		ENSP00000478272.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60154 AN: 151838 Hom.: 12621 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.396 AC: 60204 AN: 151956 Hom.: 12640 Cov.: 32 AF XY: 0.401 AC XY: 29774 AN XY: 74268

African (AFR) AF: 0.285 AC: 11828 AN: 41460

American (AMR) AF: 0.521 AC: 7958 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1429 AN: 3464

East Asian (EAS) AF: 0.651 AC: 3351 AN: 5144

South Asian (SAS) AF: 0.409 AC: 1969 AN: 4814

European-Finnish (FIN) AF: 0.379 AC: 4017 AN: 10586

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28155 AN: 67894

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.227 Hom.: 476

Bravo AF: 0.407

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.040
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3935802; hg19: chr16-81661567;