Variant 17-72947869-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_139177.4(SLC39A11):c.313G>A(p.Ala105Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00535 in 1,613,728 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 37 hom. )

Consequence

SLC39A11
NM_139177.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.879

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]

SLC39A11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0056734085).

BP6

Variant 17-72947869-C-T is Benign according to our data. Variant chr17-72947869-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 777719.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4 linkuse as main transcript	c.313G>A	p.Ala105Thr	missense_variant	5/10	ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8 linkuse as main transcript	c.313G>A	p.Ala105Thr	missense_variant	5/10	1	NM_139177.4	P4	Q8N1S5-2

Frequencies

GnomAD3 genomes

AF:

0.00411

AC:

626

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00471

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00642

Gnomad FIN

AF:

0.00669

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00542

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00472

AC:

1186

AN:

251064

Hom.:

AF XY:

0.00534

AC XY:

725

AN XY:

135694

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.00301

Gnomad ASJ exome

AF:

0.00337

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00614

Gnomad FIN exome

AF:

0.00593

Gnomad NFE exome

AF:

0.00617

Gnomad OTH exome

AF:

0.00375

GnomAD4 exome

AF:

0.00548

AC:

8007

AN:

1461446

Hom.:

Cov.:

AF XY:

0.00562

AC XY:

4089

AN XY:

727036

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00326

Gnomad4 ASJ exome

AF:

0.00314

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00655

Gnomad4 FIN exome

AF:

0.00511

Gnomad4 NFE exome

AF:

0.00586

Gnomad4 OTH exome

AF:

0.00545

GnomAD4 genome

AF:

0.00412

AC:

627

AN:

152282

Hom.:

Cov.:

AF XY:

0.00427

AC XY:

318

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00471

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00663

Gnomad4 FIN

AF:

0.00669

Gnomad4 NFE

AF:

0.00542

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.00470

Hom.:

Bravo

AF:

0.00383

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00686

AC:

ExAC

AF:

0.00484

AC:

588

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00611

EpiControl

AF:

0.00818

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 27, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.50

Cadd

Benign

Dann

Benign

0.91

Eigen

Benign

-0.61

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.11

M_CAP

Benign

0.0037

MetaRNN

Benign

0.0057

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.39

N;N;.;.;.;.

MutationTaster

Benign

0.99

N;N;N

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.45

N;N;.;.;.;.

REVEL

Benign

0.041

Sift

Benign

0.41

T;T;.;.;.;.

Sift4G

Benign

0.59

T;T;.;T;.;.

Polyphen

0.0

B;B;.;.;.;.

Vest4

0.080

MVP

0.25

MPC

0.14

ClinPred

0.0055

GERP RS

3.6

Varity_R

0.027

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over