rs2452924

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_139177.4(SLC39A11):​c.430+20128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,992 control chromosomes in the GnomAD database, including 9,276 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 0.34 ( 9276 hom., cov: 32)

Consequence

SLC39A11
NM_139177.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC39A11NM_139177.4 linkuse as main transcriptc.430+20128A>G intron_variant ENST00000255559.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC39A11ENST00000255559.8 linkuse as main transcriptc.430+20128A>G intron_variant 1 NM_139177.4 P4Q8N1S5-2

Frequencies

GnomAD3 genomes
AF:
0.337
AC:
51128
AN:
151874
Hom.:
9262
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.202
Gnomad AMI
AF:
0.242
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.320
Gnomad EAS
AF:
0.397
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.408
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.380
Gnomad OTH
AF:
0.357
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.337
AC:
51151
AN:
151992
Hom.:
9276
Cov.:
32
AF XY:
0.341
AC XY:
25290
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.202
Gnomad4 AMR
AF:
0.443
Gnomad4 ASJ
AF:
0.320
Gnomad4 EAS
AF:
0.397
Gnomad4 SAS
AF:
0.331
Gnomad4 FIN
AF:
0.408
Gnomad4 NFE
AF:
0.380
Gnomad4 OTH
AF:
0.357
Alfa
AF:
0.375
Hom.:
13924
Bravo
AF:
0.335
Asia WGS
AF:
0.361
AC:
1254
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.11
DANN
Benign
0.56
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2452924; hg19: chr17-70923763; API