rs16955705

Variant names:

• chr16-81639745-A-C
• rs16955705
• NM_198390.3:c.478-12458A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-81639745-A-C
• chr16-81639745-A-G
• chr16-81639745-A-T

Variant summary

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

The NM_198390.3(CMIP):​c.478-12458A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,056 control chromosomes in the GnomAD database, including 11,015 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 0.35 (11015 hom., cov: 32)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 13 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]

LOC105371362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.478-12458A>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.478-12458A>C		intron_variant	Intron 3 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.196-12458A>C		intron_variant	Intron 3 of 20	1		ENSP00000440401.2
CMIP	ENST00000566513.5	c.-84-12458A>C		intron_variant	Intron 2 of 19	5		ENSP00000478272.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53045 AN: 151938 Hom.: 11009 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.349 AC: 53055 AN: 152056 Hom.: 11015 Cov.: 32 AF XY: 0.348 AC XY: 25883 AN XY: 74312

African (AFR) AF: 0.123 AC: 5090 AN: 41478

American (AMR) AF: 0.400 AC: 6113 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1964 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1819 AN: 4818

European-Finnish (FIN) AF: 0.357 AC: 3768 AN: 10556

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31363 AN: 67980

Other (OTH) AF: 0.385 AC: 809 AN: 2102

Alfa AF: 0.347 Hom.: 2008

Bravo AF: 0.344

Asia WGS AF: 0.312 AC: 1085 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	3.2
DANN	Benign	0.59
PhyloP100		0.022
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: rs16955705; hg19: chr16-81673350;