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GeneBe

6-33202118-C-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006979.3(SLC39A7):c.627C>G(p.Ser209=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,612,506 control chromosomes in the GnomAD database, including 10,258 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.088 ( 741 hom., cov: 32)
Exomes 𝑓: 0.11 ( 9517 hom. )

Consequence

SLC39A7
NM_006979.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.08
Variant links:
Genes affected
SLC39A7 (HGNC:4927): (solute carrier family 39 member 7) The protein encoded by this gene transports zinc from the Golgi and endoplasmic reticulum to the cytoplasm. This transport may be important for activation of tyrosine kinases, some of which could be involved in cancer progression. Therefore, modulation of the encoded protein could be useful as a therapeutic agent against cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-33202118-C-G is Benign according to our data. Variant chr6-33202118-C-G is described in ClinVar as [Benign]. Clinvar id is 1164496.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC39A7NM_006979.3 linkuse as main transcriptc.627C>G p.Ser209= synonymous_variant 3/7 ENST00000374677.8
SLC39A7NM_001077516.2 linkuse as main transcriptc.627C>G p.Ser209= synonymous_variant 4/8
SLC39A7NM_001288777.2 linkuse as main transcriptc.252C>G p.Ser84= synonymous_variant 4/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC39A7ENST00000374677.8 linkuse as main transcriptc.627C>G p.Ser209= synonymous_variant 3/71 NM_006979.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0883
AC:
13424
AN:
152012
Hom.:
739
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0457
Gnomad AMI
AF:
0.241
Gnomad AMR
AF:
0.0700
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.0576
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.0659
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.0962
GnomAD3 exomes
AF:
0.106
AC:
25834
AN:
244624
Hom.:
1754
AF XY:
0.115
AC XY:
15457
AN XY:
133896
show subpopulations
Gnomad AFR exome
AF:
0.0404
Gnomad AMR exome
AF:
0.0553
Gnomad ASJ exome
AF:
0.128
Gnomad EAS exome
AF:
0.0688
Gnomad SAS exome
AF:
0.216
Gnomad FIN exome
AF:
0.0674
Gnomad NFE exome
AF:
0.111
Gnomad OTH exome
AF:
0.106
GnomAD4 exome
AF:
0.107
AC:
156322
AN:
1460376
Hom.:
9517
Cov.:
32
AF XY:
0.112
AC XY:
81289
AN XY:
726516
show subpopulations
Gnomad4 AFR exome
AF:
0.0467
Gnomad4 AMR exome
AF:
0.0574
Gnomad4 ASJ exome
AF:
0.131
Gnomad4 EAS exome
AF:
0.0581
Gnomad4 SAS exome
AF:
0.216
Gnomad4 FIN exome
AF:
0.0686
Gnomad4 NFE exome
AF:
0.105
Gnomad4 OTH exome
AF:
0.106
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0883
AC:
13432
AN:
152130
Hom.:
741
Cov.:
32
AF XY:
0.0889
AC XY:
6611
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0458
Gnomad4 AMR
AF:
0.0698
Gnomad4 ASJ
AF:
0.131
Gnomad4 EAS
AF:
0.0575
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.0659
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.0961
Alfa
AF:
0.111
Hom.:
745
Bravo
AF:
0.0828
Asia WGS
AF:
0.138
AC:
478
AN:
3478
EpiCase
AF:
0.118
EpiControl
AF:
0.122

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
Cadd
Benign
6.5
Dann
Benign
0.76
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs1547387; hg19: chr6-33169895; COSMIC: COSV63399674; COSMIC: COSV63399674; API