ENST00000383933.1:n.63C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000383933.1(Y_RNA):n.63C>G 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 0.2 in 152,208 control chromosomes in the GnomAD database, including 3,303 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 0.20 ( 3300 hom., cov: 32)
Exomes 𝑓: 0.26 ( 3 hom. )
Consequence
Y_RNA
ENST00000383933.1 non_coding_transcript_exon
ENST00000383933.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.10
Publications
3 publications found
Genes affected
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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| Y_RNA | ENST00000383933.1 | n.63C>G | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes 0.200 AC: 30446AN: 152056Hom.: 3292 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
30446
AN:
152056
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.265 AC: 9AN: 34Hom.: 3 Cov.: 0 AF XY: 0.273 AC XY: 6AN XY: 22 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
34
Hom.:
Cov.:
0
AF XY:
AC XY:
6
AN XY:
22
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
6
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
9
AN:
26
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.200 AC: 30490AN: 152174Hom.: 3300 Cov.: 32 AF XY: 0.196 AC XY: 14616AN XY: 74390 show subpopulations
GnomAD4 genome
AF:
AC:
30490
AN:
152174
Hom.:
Cov.:
32
AF XY:
AC XY:
14616
AN XY:
74390
show subpopulations
African (AFR)
AF:
AC:
6672
AN:
41508
American (AMR)
AF:
AC:
2845
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
814
AN:
3470
East Asian (EAS)
AF:
AC:
40
AN:
5186
South Asian (SAS)
AF:
AC:
863
AN:
4826
European-Finnish (FIN)
AF:
AC:
1930
AN:
10580
Middle Eastern (MID)
AF:
AC:
72
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16658
AN:
67990
Other (OTH)
AF:
AC:
432
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1270
2540
3809
5079
6349
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
332
664
996
1328
1660
<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:
425
AN:
3478
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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