chr13-99579319-T-G

Variant summary

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

The NR_126390.1(LINC01039):​n.450+680T>G 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 0.679 in 151,914 control chromosomes in the GnomAD database, including 35,350 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 0.68 ( 35350 hom., cov: 30)

Consequence

LINC01039
NR_126390.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.617
Variant links:
Genes affected
LINC01039 (HGNC:49027): (long intergenic non-protein coding RNA 1039)

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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01039NR_126390.1 linkuse as main transcriptn.450+680T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01039ENST00000437113.2 linkuse as main transcriptn.450+680T>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103118
AN:
151796
Hom.:
35334
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.631
Gnomad AMI
AF:
0.716
Gnomad AMR
AF:
0.758
Gnomad ASJ
AF:
0.608
Gnomad EAS
AF:
0.883
Gnomad SAS
AF:
0.695
Gnomad FIN
AF:
0.765
Gnomad MID
AF:
0.709
Gnomad NFE
AF:
0.664
Gnomad OTH
AF:
0.690
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.679
AC:
103176
AN:
151914
Hom.:
35350
Cov.:
30
AF XY:
0.688
AC XY:
51089
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.630
Gnomad4 AMR
AF:
0.759
Gnomad4 ASJ
AF:
0.608
Gnomad4 EAS
AF:
0.883
Gnomad4 SAS
AF:
0.694
Gnomad4 FIN
AF:
0.765
Gnomad4 NFE
AF:
0.664
Gnomad4 OTH
AF:
0.692
Alfa
AF:
0.692
Hom.:
6211
Bravo
AF:
0.678
Asia WGS
AF:
0.786
AC:
2734
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.1
DANN
Benign
0.32

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: rs2793772; hg19: chr13-100231573; API