rs2927307

Variant names:

• chr16-81510227-G-A
• rs2927307
• NM_198390.3:c.300+64686G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-81510227-G-A
• chr16-81510227-G-C
• chr16-81510227-G-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.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
• Publications: 6 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=-0.85).
• 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 rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+64686G>A		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2
CMIP	NM_030629.3	c.18+14733G>A		intron_variant	Intron 1 of 20		NP_085132.1
CMIP	XM_011523352.2	c.300+64686G>A		intron_variant	Intron 1 of 19		XP_011521654.1
CMIP	XM_047434717.1	c.252+14733G>A		intron_variant	Intron 2 of 21		XP_047290673.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.300+64686G>A		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.18+14733G>A		intron_variant	Intron 1 of 20	1		ENSP00000440401.2

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

African (AFR) AF: 0.725 AC: 30013 AN: 41400

American (AMR) AF: 0.740 AC: 11296 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4295 AN: 5148

South Asian (SAS) AF: 0.701 AC: 3379 AN: 4818

European-Finnish (FIN) AF: 0.543 AC: 5732 AN: 10550

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

European-Non Finnish (NFE) AF: 0.581 AC: 39469 AN: 67942

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

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
PhyloP100		-0.15
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: rs2927307; hg19: chr16-81543832;