ENST00000699074.1:c.550-4574C>A

Variant names:

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

Variant summary

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

The ENST00000699074.1(CMPK1):​c.550-4574C>A 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 0.43 (14023 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01389	NR_126355.1	n.405-3351G>T		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>A		intron_variant	Intron 5 of 5			ENSP00000514113.1
LINC01389	ENST00000420876.1	n.159-3351G>T		intron_variant	Intron 1 of 2	3
LINC01389	ENST00000828805.1	n.208-8564G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 58163 AN: 135432 Hom.: 14023 Cov.: 20

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.480

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.429 AC: 58153 AN: 135496 Hom.: 14023 Cov.: 20 AF XY: 0.429 AC XY: 27711 AN XY: 64530

African (AFR) AF: 0.254 AC: 9021 AN: 35498

American (AMR) AF: 0.427 AC: 5282 AN: 12382

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2047 AN: 3384

East Asian (EAS) AF: 0.212 AC: 899 AN: 4244

South Asian (SAS) AF: 0.448 AC: 1877 AN: 4186

European-Finnish (FIN) AF: 0.619 AC: 4639 AN: 7490

Middle Eastern (MID) AF: 0.493 AC: 136 AN: 276

European-Non Finnish (NFE) AF: 0.505 AC: 32943 AN: 65270

Other (OTH) AF: 0.462 AC: 872 AN: 1888

Alfa AF: 0.450 Hom.: 5075

Bravo AF: 0.402

Asia WGS AF: 0.294 AC: 970 AN: 3298

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	0.41
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;