chr1-47378792-G-A

Variant names:

• chr1-47378792-G-A
• rs6795
• NM_016308.3:c.*2047G>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.*2047G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,096 control chromosomes in the GnomAD database, including 14,711 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 (14711 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CMPK1 NM_016308.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 10 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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 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.*2047G>A		3_prime_UTR	Exon 6 of 6	NP_057392.1
	CMPK1	NR_046394.2		n.2813G>A		non_coding_transcript_exon	Exon 5 of 5
	CMPK1	NM_001366135.1		c.*2047G>A		3_prime_UTR	Exon 6 of 6	NP_001353064.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMPK1	ENST00000371873.10	TSL:1 MANE Select	c.*2047G>A		3_prime_UTR	Exon 6 of 6	ENSP00000360939.5
	CMPK1	ENST00000699075.1		c.*2047G>A		3_prime_UTR	Exon 6 of 6	ENSP00000514114.1
	CMPK1	ENST00000699074.1		c.549+3499G>A		intron	N/A	ENSP00000514113.1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60016 AN: 151976 Hom.: 14707 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.432

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.395 AC: 60023 AN: 152094 Hom.: 14711 Cov.: 32 AF XY: 0.397 AC XY: 29543 AN XY: 74336

African (AFR) AF: 0.105 AC: 4348 AN: 41502

American (AMR) AF: 0.418 AC: 6384 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2216 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1079 AN: 5184

South Asian (SAS) AF: 0.453 AC: 2183 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6469 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35817 AN: 67952

Other (OTH) AF: 0.433 AC: 916 AN: 2114

Alfa AF: 0.476 Hom.: 49396

Bravo AF: 0.365

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		-0.011
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: rs6795; hg19: chr1-47844464;