16-81620052-C-T

Variant names:

• chr16-81620052-C-T
• rs6564903
• NM_198390.3:c.427-824C>T

Variant summary

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

The NM_198390.3(CMIP):​c.427-824C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,026 control chromosomes in the GnomAD database, including 19,973 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 0.50 (19972 hom., cov: 32)
  • Exomes 𝑓: 0.43 (1 hom.)
• Consequence: CMIP NM_198390.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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]

ENSG00000279294 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMIP	NM_198390.3	c.427-824C>T		intron_variant	Intron 2 of 20	ENST00000537098.8	NP_938204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMIP	ENST00000537098.8	c.427-824C>T		intron_variant	Intron 2 of 20	1	NM_198390.3	ENSP00000446100.2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76643 AN: 151894 Hom.: 19945 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.518

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.505 AC: 76718 AN: 152012 Hom.: 19972 Cov.: 32 AF XY: 0.506 AC XY: 37575 AN XY: 74272

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.519

Alfa AF: 0.296 Hom.: 629

Bravo AF: 0.523

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.27
DANN	Benign	0.69

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: rs6564903; hg19: chr16-81653657;