rs11871756

Variant summary

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

The ENST00000255559.8(SLC39A11):​c.671+6545G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,200 control chromosomes in the GnomAD database, including 992 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 0.11 ( 992 hom., cov: 29)

Consequence

SLC39A11
ENST00000255559.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.199
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC39A11NM_139177.4 linkuse as main transcriptc.671+6545G>C intron_variant ENST00000255559.8 NP_631916.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC39A11ENST00000255559.8 linkuse as main transcriptc.671+6545G>C intron_variant 1 NM_139177.4 ENSP00000255559 P4Q8N1S5-2

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16636
AN:
152082
Hom.:
992
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.131
Gnomad AMI
AF:
0.0691
Gnomad AMR
AF:
0.103
Gnomad ASJ
AF:
0.0853
Gnomad EAS
AF:
0.0429
Gnomad SAS
AF:
0.0923
Gnomad FIN
AF:
0.0450
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.109
AC:
16645
AN:
152200
Hom.:
992
Cov.:
29
AF XY:
0.106
AC XY:
7883
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.131
Gnomad4 AMR
AF:
0.103
Gnomad4 ASJ
AF:
0.0853
Gnomad4 EAS
AF:
0.0430
Gnomad4 SAS
AF:
0.0915
Gnomad4 FIN
AF:
0.0450
Gnomad4 NFE
AF:
0.115
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.115
Hom.:
144
Bravo
AF:
0.115
Asia WGS
AF:
0.0720
AC:
248
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.68
DANN
Benign
0.23

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: rs11871756; hg19: chr17-70726244; API