rs878845

Variant summary

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

The ENST00000456653.6(LINC01473):​n.1050C>T 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 0.67 in 149,984 control chromosomes in the GnomAD database, including 33,773 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 0.67 ( 33773 hom., cov: 27)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LINC01473
ENST00000456653.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0690
Variant links:
Genes affected
LINC01473 (HGNC:51109): (long intergenic non-protein coding RNA 1473)

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01473ENST00000456653.6 linkn.1050C>T non_coding_transcript_exon_variant Exon 3 of 3 3
LINC01473ENST00000655126.1 linkn.1422C>T non_coding_transcript_exon_variant Exon 9 of 9
LINC01473ENST00000656786.1 linkn.1089C>T non_coding_transcript_exon_variant Exon 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
100460
AN:
149894
Hom.:
33761
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.618
Gnomad AMI
AF:
0.787
Gnomad AMR
AF:
0.686
Gnomad ASJ
AF:
0.734
Gnomad EAS
AF:
0.504
Gnomad SAS
AF:
0.641
Gnomad FIN
AF:
0.624
Gnomad MID
AF:
0.619
Gnomad NFE
AF:
0.715
Gnomad OTH
AF:
0.674
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.670
AC:
100504
AN:
149984
Hom.:
33773
Cov.:
27
AF XY:
0.663
AC XY:
48426
AN XY:
73084
show subpopulations
Gnomad4 AFR
AF:
0.618
Gnomad4 AMR
AF:
0.686
Gnomad4 ASJ
AF:
0.734
Gnomad4 EAS
AF:
0.505
Gnomad4 SAS
AF:
0.642
Gnomad4 FIN
AF:
0.624
Gnomad4 NFE
AF:
0.715
Gnomad4 OTH
AF:
0.668
Alfa
AF:
0.667
Hom.:
4023
Bravo
AF:
0.669
Asia WGS
AF:
0.557
AC:
1929
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.1
DANN
Benign
0.66

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: rs878845; hg19: chr2-186897647; API