1-47388842-C-T

Position:

• chr1-47388842-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.405-2486G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 152,224 control chromosomes in the GnomAD database, including 154 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 0.027 (154 hom., cov: 32)
• Consequence: LINC01389 NR_126355.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01389	NR_126355.1	n.405-2486G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01389	ENST00000420876.1	n.159-2486G>A		intron_variant, non_coding_transcript_variant		3
CMPK1	ENST00000699074.1	c.550-5439C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4040 AN: 152106 Hom.: 152 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0381

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0267 AC: 4063 AN: 152224 Hom.: 154 Cov.: 32 AF XY: 0.0305 AC XY: 2273 AN XY: 74418

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.0177

Gnomad4 ASJ AF: 0.0188

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0937

Gnomad4 FIN AF: 0.0381

Gnomad4 NFE AF: 0.00450

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0115 Hom.: 136

Bravo AF: 0.0251

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17103186; hg19: chr1-47854514;