rs4492666

chr1-47335173-A-Cchr1-47335173-A-T

Variant summary

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

The NM_016308.3(CMPK1):c.171+1057A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,032 control chromosomes in the GnomAD database, including 27,582 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 0.58 (27582 hom., cov: 31)
• Consequence: CMPK1 NM_016308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMPK1	NM_016308.3	c.171+1057A>C		intron_variant		ENST00000371873.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMPK1	ENST00000371873.10	c.171+1057A>C		intron_variant		1	NM_016308.3	P1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87904 AN: 151916 Hom.: 27548 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.579 AC: 87983 AN: 152032 Hom.: 27582 Cov.: 31 AF XY: 0.572 AC XY: 42486 AN XY: 74310

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.537

Alfa AF: 0.522 Hom.: 3839

Bravo AF: 0.608

Asia WGS AF: 0.507 AC: 1767 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	0.52
Dann	Benign	0.76

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: rs4492666; hg19: chr1-47800845;