rs12119783

Positions:

• chr1-47389707-C-A
• chr1-47389707-C-G
• chr1-47389707-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_126355.1(LINC01389):​n.405-3351G>T variant causes a intron, non coding transcript 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: LINC01389 NR_126355.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

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

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=-0.83).
• 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/exons	MANE	Protein	UniProt
LINC01389	NR_126355.1	n.405-3351G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01389	ENST00000420876.1	n.159-3351G>T		intron_variant, non_coding_transcript_variant		3
CMPK1	ENST00000699074.1	c.550-4574C>A		intron_variant				ENSP00000514113

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

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.462

Alfa AF: 0.415 Hom.: 2448

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12119783; hg19: chr1-47855379;