rs12119783

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
LINC01389NR_126355.1 linkuse as main transcriptn.405-3351G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01389ENST00000420876.1 linkuse as main transcriptn.159-3351G>T intron_variant, non_coding_transcript_variant 3
CMPK1ENST00000699074.1 linkuse as main transcriptc.550-4574C>A intron_variant ENSP00000514113

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12119783; hg19: chr1-47855379; API