chr1-47377105-C-T

Position:

• chr1-47377105-C-T

Variant summary

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

The NM_016308.3(CMPK1):​c.*360C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 163,658 control chromosomes in the GnomAD database, including 16,157 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 0.39 (14665 hom., cov: 32)
  • Exomes 𝑓: 0.49 (1492 hom.)
• Consequence: CMPK1 NM_016308.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

CMPK1 (HGNC:18170): (cytidine/uridine monophosphate kinase 1) This gene encodes one of the enzymes required for cellular nucleic acid biosynthesis. This enzyme catalyzes the transfer of a phosphate group from ATP to CMP, UMP, or dCMP, to form the corresponding diphosphate nucleotide. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMPK1	NM_016308.3	c.*360C>T		3_prime_UTR_variant	6/6	ENST00000371873.10	NP_057392.1
CMPK1	NM_001136140.2	c.*360C>T		3_prime_UTR_variant	5/5		NP_001129612.1
CMPK1	NM_001366135.1	c.*360C>T		3_prime_UTR_variant	6/6		NP_001353064.1
CMPK1	NR_046394.2	n.1126C>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMPK1	ENST00000371873.10	c.*360C>T		3_prime_UTR_variant	6/6	1	NM_016308.3	ENSP00000360939	P1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59630 AN: 151850 Hom.: 14661 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.490 AC: 5731 AN: 11690 Hom.: 1492 Cov.: 0 AF XY: 0.494 AC XY: 2951 AN XY: 5976

Gnomad4 AFR exome AF: 0.0997

Gnomad4 AMR exome AF: 0.411

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.245

Gnomad4 SAS exome AF: 0.432

Gnomad4 FIN exome AF: 0.601

Gnomad4 NFE exome AF: 0.533

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.392 AC: 59631 AN: 151968 Hom.: 14665 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74258

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.435

Alfa AF: 0.492 Hom.: 18104

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1044457; hg19: chr1-47842777;