GeneBe

rs1085832

Variant names:

Variant summary

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

The ENST00000646678.1(ENSG00000285201):​n.-103C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,206 control chromosomes in the GnomAD database, including 49,233 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 ( 49220 hom., cov: 32)
Exomes 𝑓: 0.82 ( 13 hom. )

Consequence

ENSG00000285201
ENST00000646678.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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
ENSG00000285201ENST00000646678.1 linkn.-103C>T upstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.801
AC:
121765
AN:
152048
Hom.:
49184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.704
Gnomad AMR
AF:
0.813
Gnomad ASJ
AF:
0.732
Gnomad EAS
AF:
0.900
Gnomad SAS
AF:
0.754
Gnomad FIN
AF:
0.773
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.747
Gnomad OTH
AF:
0.788
GnomAD4 exome
AF:
0.825
AC:
33
AN:
40
Hom.:
13
AF XY:
0.813
AC XY:
26
AN XY:
32
show subpopulations
African (AFR)
AF:
1.00
AC:
2
AN:
2
American (AMR)
AF:
1.00
AC:
2
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
1.00
AC:
2
AN:
2
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.750
AC:
3
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.821
AC:
23
AN:
28
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
1
2
2
3
4
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:
0.801
AC:
121846
AN:
152166
Hom.:
49220
Cov.:
32
AF XY:
0.803
AC XY:
59700
AN XY:
74376
show subpopulations
African (AFR)
AF:
0.895
AC:
37191
AN:
41546
American (AMR)
AF:
0.812
AC:
12421
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.732
AC:
2541
AN:
3472
East Asian (EAS)
AF:
0.900
AC:
4632
AN:
5148
South Asian (SAS)
AF:
0.753
AC:
3635
AN:
4828
European-Finnish (FIN)
AF:
0.773
AC:
8182
AN:
10582
Middle Eastern (MID)
AF:
0.684
AC:
201
AN:
294
European-Non Finnish (NFE)
AF:
0.747
AC:
50761
AN:
67988
Other (OTH)
AF:
0.778
AC:
1641
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1246
2492
3739
4985
6231
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
870
1740
2610
3480
4350
<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:
0.770
Hom.:
5612
Bravo
AF:
0.810
Asia WGS
AF:
0.787
AC:
2736
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.34
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs566830; hg19: chr1-84504109; COSMIC: COSV59966700; API