chr1-47334327-C-A

Variant names:

• chr1-47334327-C-A
• rs4600090
• NM_016308.3:c.171+211C>A

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+211C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,034 control chromosomes in the GnomAD database, including 1,153 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 0.11 (1153 hom., cov: 32)
• Consequence: CMPK1 NM_016308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 6 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016308.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMPK1	NM_016308.3	MANE Select	c.171+211C>A		intron	N/A	NP_057392.1
	CMPK1	NM_001366135.1		c.75+211C>A		intron	N/A	NP_001353064.1
	CMPK1	NM_001136140.2		c.171+211C>A		intron	N/A	NP_001129612.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMPK1	ENST00000371873.10	TSL:1 MANE Select	c.171+211C>A		intron	N/A	ENSP00000360939.5
	CMPK1	ENST00000699074.1		c.75+211C>A		intron	N/A	ENSP00000514113.1
	CMPK1	ENST00000699075.1		c.75+211C>A		intron	N/A	ENSP00000514114.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16437 AN: 151924 Hom.: 1145 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.108 AC: 16461 AN: 152034 Hom.: 1153 Cov.: 32 AF XY: 0.108 AC XY: 8045 AN XY: 74320

African (AFR) AF: 0.0958 AC: 3980 AN: 41530

American (AMR) AF: 0.240 AC: 3661 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1156 AN: 5126

South Asian (SAS) AF: 0.0624 AC: 301 AN: 4822

European-Finnish (FIN) AF: 0.0586 AC: 620 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0933 AC: 6334 AN: 67920

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.0475 Hom.: 68

Bravo AF: 0.124

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-1.0
PromoterAI		0.052	Neutral
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: rs4600090; hg19: chr1-47799999;