16-81516103-C-T

Variant names:

• chr16-81516103-C-T
• rs2966097
• NM_198390.3:c.300+70562C>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+70562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,062 control chromosomes in the GnomAD database, including 41,901 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 0.73 (41901 hom., cov: 31)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.300+70562C>T		intron_variant	Intron 1 of 20	ENST00000537098.8	NP_938204.2
CMIP	NM_030629.3	c.18+20609C>T		intron_variant	Intron 1 of 20		NP_085132.1
CMIP	XM_011523352.2	c.300+70562C>T		intron_variant	Intron 1 of 19		XP_011521654.1
CMIP	XM_047434717.1	c.252+20609C>T		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+70562C>T		intron_variant	Intron 1 of 20	1	NM_198390.3	ENSP00000446100.2
CMIP	ENST00000539778.6	c.18+20609C>T		intron_variant	Intron 1 of 20	1		ENSP00000440401.2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111526 AN: 151942 Hom.: 41840 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.734 AC: 111649 AN: 152062 Hom.: 41901 Cov.: 31 AF XY: 0.733 AC XY: 54480 AN XY: 74304

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.727

Alfa AF: 0.671 Hom.: 53486

Bravo AF: 0.756

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2

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: rs2966097; hg19: chr16-81549708;