rs4492666

Variant names:

• chr1-47335173-A-C
• rs4492666
• NM_016308.3:c.171+1057A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-47335173-A-C
• chr1-47335173-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CMPK1	NM_016308.3	c.171+1057A>C		intron_variant	Intron 1 of 5	ENST00000371873.10	NP_057392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMPK1	ENST00000371873.10	c.171+1057A>C		intron_variant	Intron 1 of 5	1	NM_016308.3	ENSP00000360939.5

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

African (AFR) AF: 0.832 AC: 34521 AN: 41478

American (AMR) AF: 0.569 AC: 8688 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2850 AN: 5162

South Asian (SAS) AF: 0.448 AC: 2162 AN: 4822

European-Finnish (FIN) AF: 0.357 AC: 3765 AN: 10558

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33060 AN: 67966

Other (OTH) AF: 0.537 AC: 1135 AN: 2112

Alfa AF: 0.530 Hom.: 37399

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
PhyloP100		-0.21
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: rs4492666; hg19: chr1-47800845;