1-47389707-C-T

Variant names:

• chr1-47389707-C-T
• rs12119783
• ENST00000699074.1:c.550-4574C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000699074.1(CMPK1):​c.550-4574C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000022 (0 hom., cov: 20)
• Consequence: CMPK1 ENST00000699074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 3 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]

LINC01389 (HGNC:50661): (long intergenic non-protein coding RNA 1389)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01389	NR_126355.1	n.405-3351G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMPK1	ENST00000699074.1	c.550-4574C>T		intron_variant	Intron 5 of 5			ENSP00000514113.1
LINC01389	ENST00000420876.1	n.159-3351G>A		intron_variant	Intron 1 of 2	3
LINC01389	ENST00000828805.1	n.208-8564G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000221 AC: 3 AN: 135602 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000713

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000221 AC: 3 AN: 135666 Hom.: 0 Cov.: 20 AF XY: 0.0000155 AC XY: 1 AN XY: 64622

African (AFR) AF: 0.00 AC: 0 AN: 35550

American (AMR) AF: 0.00 AC: 0 AN: 12404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3386

East Asian (EAS) AF: 0.00 AC: 0 AN: 4246

South Asian (SAS) AF: 0.000716 AC: 3 AN: 4190

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7506

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 65340

Other (OTH) AF: 0.00 AC: 0 AN: 1888

Alfa AF: 0.00 Hom.: 5075

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.57
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12119783; hg19: chr1-47855379;