ENST00000647807.1:n.464-16206C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000647807.1(LUCAT1):n.464-16206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 148,610 control chromosomes in the GnomAD database, including 48,549 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 0.80 ( 48549 hom., cov: 25)
Consequence
LUCAT1
ENST00000647807.1 intron
ENST00000647807.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.505
Publications
3 publications found
Genes affected
LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC107986432 | XR_001742795.2 | n.611+3447C>G | intron_variant | Intron 1 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.805 AC: 119512AN: 148506Hom.: 48521 Cov.: 25 show subpopulations
GnomAD3 genomes
AF:
AC:
119512
AN:
148506
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.805 AC: 119588AN: 148610Hom.: 48549 Cov.: 25 AF XY: 0.803 AC XY: 57963AN XY: 72196 show subpopulations
GnomAD4 genome
AF:
AC:
119588
AN:
148610
Hom.:
Cov.:
25
AF XY:
AC XY:
57963
AN XY:
72196
show subpopulations
African (AFR)
AF:
AC:
28496
AN:
40272
American (AMR)
AF:
AC:
10913
AN:
14564
Ashkenazi Jewish (ASJ)
AF:
AC:
3149
AN:
3464
East Asian (EAS)
AF:
AC:
2774
AN:
4850
South Asian (SAS)
AF:
AC:
3586
AN:
4692
European-Finnish (FIN)
AF:
AC:
8619
AN:
9698
Middle Eastern (MID)
AF:
AC:
239
AN:
288
European-Non Finnish (NFE)
AF:
AC:
59299
AN:
67800
Other (OTH)
AF:
AC:
1690
AN:
2076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1080
2160
3240
4320
5400
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
872
1744
2616
3488
4360
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2310
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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