rs6795

Positions:

• chr1-47378792-G-A
• chr1-47378792-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMPK1	NM_016308.3	c.*2047G>A		3_prime_UTR_variant	6/6	ENST00000371873.10
CMPK1	NM_001136140.2	c.*2047G>A		3_prime_UTR_variant	5/5
CMPK1	NM_001366135.1	c.*2047G>A		3_prime_UTR_variant	6/6
CMPK1	NR_046394.2	n.2813G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMPK1	ENST00000371873.10	c.*2047G>A		3_prime_UTR_variant	6/6	1	NM_016308.3	P1
CMPK1	ENST00000699075.1	c.*2047G>A		3_prime_UTR_variant	6/6
CMPK1	ENST00000699074.1	c.549+3499G>A		intron_variant

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

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.433

Alfa AF: 0.507 Hom.: 32154

Bravo AF: 0.365

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.5
DANN	Benign	0.64

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: rs6795; hg19: chr1-47844464;