rs10514518

chr16-81546222-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CMIP	NM_198390.3	c.301-61345C>T		intron_variant		ENST00000537098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.301-61345C>T		intron_variant		1	NM_198390.3	P1
CMIP	ENST00000539778.6	c.18+50728C>T		intron_variant		1

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

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.589

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514518; hg19: chr16-81579827;