GeneBe

20-5113878-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000516558.1(Y_RNA):​n.*115C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,380 control chromosomes in the GnomAD database, including 2,586 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 0.16 ( 2586 hom., cov: 33)
Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

Y_RNA
ENST00000516558.1 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

3 publications found
Variant links:
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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 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_RNAENST00000516558.1 linkn.*115C>G downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23586
AN:
151256
Hom.:
2580
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.307
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.109
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.000777
Gnomad SAS
AF:
0.0584
Gnomad FIN
AF:
0.0600
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.109
Gnomad OTH
AF:
0.155
GnomAD4 exome
AF:
0.125
AC:
1
AN:
8
Hom.:
0
AF XY:
0.250
AC XY:
1
AN XY:
4
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.500
AC:
1
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
4
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.156
AC:
23619
AN:
151372
Hom.:
2586
Cov.:
33
AF XY:
0.153
AC XY:
11276
AN XY:
73894
show subpopulations
African (AFR)
AF:
0.307
AC:
12689
AN:
41362
American (AMR)
AF:
0.109
AC:
1660
AN:
15184
Ashkenazi Jewish (ASJ)
AF:
0.148
AC:
513
AN:
3462
East Asian (EAS)
AF:
0.000779
AC:
4
AN:
5134
South Asian (SAS)
AF:
0.0587
AC:
272
AN:
4632
European-Finnish (FIN)
AF:
0.0600
AC:
629
AN:
10478
Middle Eastern (MID)
AF:
0.136
AC:
40
AN:
294
European-Non Finnish (NFE)
AF:
0.109
AC:
7372
AN:
67824
Other (OTH)
AF:
0.153
AC:
321
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
949
1899
2848
3798
4747
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
238
476
714
952
1190
<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:
0.127
Hom.:
221
Bravo
AF:
0.165
Asia WGS
AF:
0.0440
AC:
156
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
0.16
DANN
Benign
0.69
PhyloP100
-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3730453; hg19: chr20-5094524; API