chr1-47346428-C-T

Variant names:

• chr1-47346428-C-T
• rs9436883
• NM_016308.3:c.171+12312C>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+12312C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 152,136 control chromosomes in the GnomAD database, including 144 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 0.024 (144 hom., cov: 32)
• Consequence: CMPK1 NM_016308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMPK1	NM_016308.3	c.171+12312C>T		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+12312C>T		intron_variant	Intron 1 of 5	1	NM_016308.3	ENSP00000360939.5

Frequencies

GnomAD3 genomes AF: 0.0240 AC: 3644 AN: 152020 Hom.: 138 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00469

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0241 AC: 3674 AN: 152136 Hom.: 144 Cov.: 32 AF XY: 0.0280 AC XY: 2086 AN XY: 74374

African (AFR) AF: 0.0260 AC: 1079 AN: 41530

American (AMR) AF: 0.0178 AC: 272 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5158

South Asian (SAS) AF: 0.0945 AC: 455 AN: 4814

European-Finnish (FIN) AF: 0.0387 AC: 410 AN: 10586

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00469 AC: 319 AN: 68004

Other (OTH) AF: 0.0247 AC: 52 AN: 2108

Alfa AF: 0.0135 Hom.: 6

Bravo AF: 0.0219

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.35
PhyloP100		0.18
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: rs9436883; hg19: chr1-47812100;