rs2927307

chr16-81510227-G-Achr16-81510227-G-Cchr16-81510227-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198390.3(CMIP):c.300+64686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,912 control chromosomes in the GnomAD database, including 32,499 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 0.65 (32499 hom., cov: 30)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMIP	NM_198390.3	c.300+64686G>A		intron_variant		ENST00000537098.8
CMIP	NM_030629.3	c.18+14733G>A		intron_variant
CMIP	XM_011523352.2	c.300+64686G>A		intron_variant
CMIP	XM_047434717.1	c.252+14733G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMIP	ENST00000537098.8	c.300+64686G>A		intron_variant		1	NM_198390.3	P1
CMIP	ENST00000539778.6	c.18+14733G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98489 AN: 151794 Hom.: 32455 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.649 AC: 98595 AN: 151912 Hom.: 32499 Cov.: 30 AF XY: 0.653 AC XY: 48507 AN XY: 74240

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.662

Alfa AF: 0.507 Hom.: 1558

Bravo AF: 0.664

Asia WGS AF: 0.744 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.56
Dann	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2927307; hg19: chr16-81543832;