17-72792267-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_139177.4(SLC39A11):c.602-55548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,058 control chromosomes in the GnomAD database, including 27,261 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 0.58 ( 27261 hom., cov: 32)
Consequence
SLC39A11
NM_139177.4 intron
NM_139177.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.289
Publications
4 publications found
Genes affected
SLC39A11 (HGNC:14463): (solute carrier family 39 member 11) Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.585 AC: 88898AN: 151940Hom.: 27249 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
88898
AN:
151940
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.585 AC: 88940AN: 152058Hom.: 27261 Cov.: 32 AF XY: 0.579 AC XY: 43019AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
88940
AN:
152058
Hom.:
Cov.:
32
AF XY:
AC XY:
43019
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
18243
AN:
41470
American (AMR)
AF:
AC:
8007
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
2313
AN:
3468
East Asian (EAS)
AF:
AC:
1484
AN:
5154
South Asian (SAS)
AF:
AC:
2487
AN:
4830
European-Finnish (FIN)
AF:
AC:
7159
AN:
10580
Middle Eastern (MID)
AF:
AC:
195
AN:
294
European-Non Finnish (NFE)
AF:
AC:
47231
AN:
67970
Other (OTH)
AF:
AC:
1238
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1799
3598
5396
7195
8994
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
738
1476
2214
2952
3690
<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:
1427
AN:
3478
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.