chr1-47367541-A-C

Variant names:

• chr1-47367541-A-C
• rs11211524
• NM_016308.3:c.172-928A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016308.3(CMPK1):​c.172-928A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,116 control chromosomes in the GnomAD database, including 6,240 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 0.26 (6240 hom., cov: 32)
• Consequence: CMPK1 NM_016308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMPK1	NM_016308.3	c.172-928A>C		intron_variant	Intron 1 of 5	ENST00000371873.10	NP_057392.1
CMPK1	NM_001366135.1	c.76-928A>C		intron_variant	Intron 1 of 5		NP_001353064.1
CMPK1	NM_001136140.2	c.172-5414A>C		intron_variant	Intron 1 of 4		NP_001129612.1
CMPK1	NR_046394.2	n.328-928A>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMPK1	ENST00000371873.10	c.172-928A>C		intron_variant	Intron 1 of 5	1	NM_016308.3	ENSP00000360939.5

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39125 AN: 151998 Hom.: 6229 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.257 AC: 39169 AN: 152116 Hom.: 6240 Cov.: 32 AF XY: 0.258 AC XY: 19191 AN XY: 74364

African (AFR) AF: 0.402 AC: 16667 AN: 41452

American (AMR) AF: 0.320 AC: 4887 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.543 AC: 2806 AN: 5172

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10608

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11395 AN: 68010

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.218 Hom.: 7533

Bravo AF: 0.283

Asia WGS AF: 0.360 AC: 1254 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		1.4
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: rs11211524; hg19: chr1-47833213;