chr5-16441477-G-A

Variant summary

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

The ENST00000773338.1(ENSG00000300672):​n.-234G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,180 control chromosomes in the GnomAD database, including 48,865 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 ( 48865 hom., cov: 33)

Consequence

ENSG00000300672
ENST00000773338.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

4 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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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
ENSG00000300672ENST00000773338.1 linkn.-234G>A upstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.799
AC:
121479
AN:
152062
Hom.:
48806
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.897
Gnomad AMI
AF:
0.778
Gnomad AMR
AF:
0.773
Gnomad ASJ
AF:
0.767
Gnomad EAS
AF:
0.694
Gnomad SAS
AF:
0.672
Gnomad FIN
AF:
0.793
Gnomad MID
AF:
0.737
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.787
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.799
AC:
121607
AN:
152180
Hom.:
48865
Cov.:
33
AF XY:
0.798
AC XY:
59333
AN XY:
74398
show subpopulations
African (AFR)
AF:
0.897
AC:
37254
AN:
41526
American (AMR)
AF:
0.772
AC:
11806
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.767
AC:
2663
AN:
3472
East Asian (EAS)
AF:
0.694
AC:
3583
AN:
5162
South Asian (SAS)
AF:
0.673
AC:
3245
AN:
4824
European-Finnish (FIN)
AF:
0.793
AC:
8403
AN:
10592
Middle Eastern (MID)
AF:
0.748
AC:
220
AN:
294
European-Non Finnish (NFE)
AF:
0.766
AC:
52059
AN:
68004
Other (OTH)
AF:
0.789
AC:
1668
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1208
2416
3625
4833
6041
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
868
1736
2604
3472
4340
<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:
0.789
Hom.:
8266
Bravo
AF:
0.803
Asia WGS
AF:
0.737
AC:
2562
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.065
DANN
Benign
0.18
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: rs171817; hg19: chr5-16441586; API