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GeneBe

18-55776198-C-T

Variant summary

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

The NR_145452.1(LINC01415):n.4604G>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 0.887 in 152,208 control chromosomes in the GnomAD database, including 60,216 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 0.89 ( 60216 hom., cov: 31)

Consequence

LINC01415
NR_145452.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.541
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC01415NR_145452.1 linkuse as main transcriptn.4604G>A non_coding_transcript_exon_variant 2/2
LOC105372130XR_007066382.1 linkuse as main transcriptn.329-8701C>T intron_variant, non_coding_transcript_variant
LINC01415NR_145453.1 linkuse as main transcriptn.4106G>A non_coding_transcript_exon_variant 2/2
LINC01415NR_145454.1 linkuse as main transcriptn.3896G>A non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000654829.1 linkuse as main transcriptn.157-8701C>T intron_variant, non_coding_transcript_variant
ENST00000587346.1 linkuse as main transcriptn.519+3427C>T intron_variant, non_coding_transcript_variant 4
ENST00000589662.1 linkuse as main transcriptn.218-8701C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.887
AC:
134963
AN:
152090
Hom.:
60154
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.970
Gnomad AMI
AF:
0.916
Gnomad AMR
AF:
0.923
Gnomad ASJ
AF:
0.770
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.788
Gnomad FIN
AF:
0.872
Gnomad MID
AF:
0.873
Gnomad NFE
AF:
0.836
Gnomad OTH
AF:
0.892
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.887
AC:
135081
AN:
152208
Hom.:
60216
Cov.:
31
AF XY:
0.889
AC XY:
66120
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.970
Gnomad4 AMR
AF:
0.923
Gnomad4 ASJ
AF:
0.770
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.786
Gnomad4 FIN
AF:
0.872
Gnomad4 NFE
AF:
0.836
Gnomad4 OTH
AF:
0.895
Alfa
AF:
0.834
Hom.:
2553
Bravo
AF:
0.900
Asia WGS
AF:
0.913
AC:
3175
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.59
Dann
Benign
0.64

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: rs931040; hg19: chr18-53443429; API