rs17103186

Variant names:

• chr1-47388842-C-T
• rs17103186
• ENST00000828812.1:n.284G>A

Variant summary

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

The ENST00000828812.1(LINC01389):​n.284G>A variant causes a non coding transcript exon 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 ENST00000828812.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01389	NR_126355.1	n.405-2486G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01389	ENST00000828812.1	n.284G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC01389	ENST00000828813.1	n.267G>A		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01389	ENST00000828814.1	n.40G>A		non_coding_transcript_exon_variant	Exon 1 of 3

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

African (AFR) AF: 0.0356 AC: 1479 AN: 41542

American (AMR) AF: 0.0177 AC: 271 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 65 AN: 3464

East Asian (EAS) AF: 0.196 AC: 1015 AN: 5168

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4826

European-Finnish (FIN) AF: 0.0381 AC: 404 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00450 AC: 306 AN: 68020

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0134 Hom.: 367

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
PhyloP100		0.0040
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17103186; hg19: chr1-47854514;