NM_017613.4:c.1351-715C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017613.4(DONSON):c.1351-715C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 147,266 control chromosomes in the GnomAD database, including 11,073 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 0.38 ( 11073 hom., cov: 23)
Consequence
DONSON
NM_017613.4 intron
NM_017613.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.249
Publications
4 publications found
Genes affected
DONSON (HGNC:2993): (DNA replication fork stabilization factor DONSON) This gene lies downstream of the SON gene and spans 10 kb on chromosome 21. The function of this gene is unknown. [provided by RefSeq, Jul 2008]
DONSON Gene-Disease associations (from GenCC):
- microcephaly, short stature, and limb abnormalitiesInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.385 AC: 56650AN: 147150Hom.: 11086 Cov.: 23 show subpopulations
GnomAD3 genomes
AF:
AC:
56650
AN:
147150
Hom.:
Cov.:
23
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: 0.385 AC: 56628AN: 147266Hom.: 11073 Cov.: 23 AF XY: 0.387 AC XY: 27724AN XY: 71716 show subpopulations
GnomAD4 genome
AF:
AC:
56628
AN:
147266
Hom.:
Cov.:
23
AF XY:
AC XY:
27724
AN XY:
71716
show subpopulations
African (AFR)
AF:
AC:
13695
AN:
39664
American (AMR)
AF:
AC:
6080
AN:
14776
Ashkenazi Jewish (ASJ)
AF:
AC:
1146
AN:
3414
East Asian (EAS)
AF:
AC:
2874
AN:
4912
South Asian (SAS)
AF:
AC:
2000
AN:
4584
European-Finnish (FIN)
AF:
AC:
3796
AN:
9852
Middle Eastern (MID)
AF:
AC:
87
AN:
268
European-Non Finnish (NFE)
AF:
AC:
25948
AN:
66900
Other (OTH)
AF:
AC:
710
AN:
2006
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1546
3091
4637
6182
7728
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
560
1120
1680
2240
2800
<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:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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