17-72792267-G-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.289

Publications

4 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC39A11NM_139177.4 linkc.602-55548C>T intron_variant Intron 6 of 9 ENST00000255559.8 NP_631916.2 Q8N1S5-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC39A11ENST00000255559.8 linkc.602-55548C>T intron_variant Intron 6 of 9 1 NM_139177.4 ENSP00000255559.3 Q8N1S5-2

Frequencies

GnomAD3 genomes
AF:
0.585
AC:
88898
AN:
151940
Hom.:
27249
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.440
Gnomad AMI
AF:
0.642
Gnomad AMR
AF:
0.525
Gnomad ASJ
AF:
0.667
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.514
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.658
Gnomad NFE
AF:
0.695
Gnomad OTH
AF:
0.590
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.585
AC:
88940
AN:
152058
Hom.:
27261
Cov.:
32
AF XY:
0.579
AC XY:
43019
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.440
AC:
18243
AN:
41470
American (AMR)
AF:
0.524
AC:
8007
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.667
AC:
2313
AN:
3468
East Asian (EAS)
AF:
0.288
AC:
1484
AN:
5154
South Asian (SAS)
AF:
0.515
AC:
2487
AN:
4830
European-Finnish (FIN)
AF:
0.677
AC:
7159
AN:
10580
Middle Eastern (MID)
AF:
0.663
AC:
195
AN:
294
European-Non Finnish (NFE)
AF:
0.695
AC:
47231
AN:
67970
Other (OTH)
AF:
0.587
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:
0.609
Hom.:
9907
Bravo
AF:
0.566
Asia WGS
AF:
0.410
AC:
1427
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.67
PhyloP100
-0.29
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2567519; hg19: chr17-70788406; API