chr16-81546222-C-T

Variant names:

• chr16-81546222-C-T
• rs10514518
• NM_198390.3:c.301-61345C>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.301-61345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,984 control chromosomes in the GnomAD database, including 27,100 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 0.58 (27100 hom., cov: 31)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.301-61345C>T		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.301-61345C>T		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.18+50728C>T		intron_variant	Intron 1 of 20	1		ENSP00000440401.2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87485 AN: 151866 Hom.: 27097 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.576 AC: 87520 AN: 151984 Hom.: 27100 Cov.: 31 AF XY: 0.579 AC XY: 43024 AN XY: 74296

African (AFR) AF: 0.338 AC: 14013 AN: 41470

American (AMR) AF: 0.622 AC: 9494 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2523 AN: 5154

South Asian (SAS) AF: 0.589 AC: 2836 AN: 4816

European-Finnish (FIN) AF: 0.715 AC: 7539 AN: 10544

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46792 AN: 67942

Other (OTH) AF: 0.589 AC: 1244 AN: 2112

Alfa AF: 0.633 Hom.: 5493

Bravo AF: 0.558

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.44
PhyloP100		-1.0
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: rs10514518; hg19: chr16-81579827;