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GeneBe

4-41990660-C-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006345.4(SLC30A9):c.9C>G(p.Pro3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,602,308 control chromosomes in the GnomAD database, including 532,853 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 40037 hom., cov: 35)
Exomes 𝑓: 0.82 ( 492816 hom. )

Consequence

SLC30A9
NM_006345.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.311
Variant links:
Genes affected
SLC30A9 (HGNC:1329): (solute carrier family 30 member 9) Predicted to enable nuclear receptor coactivator activity. Involved in cellular zinc ion homeostasis and zinc ion transport. Located in several cellular components, including cytoplasmic vesicle; cytoskeleton; and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-41990660-C-G is Benign according to our data. Variant chr4-41990660-C-G is described in ClinVar as [Benign]. Clinvar id is 1242979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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=0.311 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC30A9NM_006345.4 linkuse as main transcriptc.9C>G p.Pro3= synonymous_variant 1/18 ENST00000264451.12
SLC30A9XM_047449525.1 linkuse as main transcriptc.9C>G p.Pro3= synonymous_variant 1/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC30A9ENST00000264451.12 linkuse as main transcriptc.9C>G p.Pro3= synonymous_variant 1/181 NM_006345.4 P1
SLC30A9ENST00000510460.1 linkuse as main transcriptn.134C>G non_coding_transcript_exon_variant 1/42
SLC30A9ENST00000513699.5 linkuse as main transcriptc.9C>G p.Pro3= synonymous_variant, NMD_transcript_variant 1/192

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.689
AC:
104911
AN:
152160
Hom.:
40022
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.330
Gnomad AMI
AF:
0.917
Gnomad AMR
AF:
0.803
Gnomad ASJ
AF:
0.801
Gnomad EAS
AF:
0.963
Gnomad SAS
AF:
0.856
Gnomad FIN
AF:
0.831
Gnomad MID
AF:
0.759
Gnomad NFE
AF:
0.818
Gnomad OTH
AF:
0.727
GnomAD3 exomes
AF:
0.810
AC:
193996
AN:
239426
Hom.:
80971
AF XY:
0.818
AC XY:
106963
AN XY:
130762
show subpopulations
Gnomad AFR exome
AF:
0.313
Gnomad AMR exome
AF:
0.853
Gnomad ASJ exome
AF:
0.798
Gnomad EAS exome
AF:
0.970
Gnomad SAS exome
AF:
0.863
Gnomad FIN exome
AF:
0.828
Gnomad NFE exome
AF:
0.821
Gnomad OTH exome
AF:
0.821
GnomAD4 exome
AF:
0.820
AC:
1188670
AN:
1450030
Hom.:
492816
Cov.:
33
AF XY:
0.821
AC XY:
591673
AN XY:
720240
show subpopulations
Gnomad4 AFR exome
AF:
0.316
Gnomad4 AMR exome
AF:
0.846
Gnomad4 ASJ exome
AF:
0.797
Gnomad4 EAS exome
AF:
0.969
Gnomad4 SAS exome
AF:
0.863
Gnomad4 FIN exome
AF:
0.826
Gnomad4 NFE exome
AF:
0.827
Gnomad4 OTH exome
AF:
0.798
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.689
AC:
104969
AN:
152278
Hom.:
40037
Cov.:
35
AF XY:
0.696
AC XY:
51839
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.331
Gnomad4 AMR
AF:
0.803
Gnomad4 ASJ
AF:
0.801
Gnomad4 EAS
AF:
0.963
Gnomad4 SAS
AF:
0.856
Gnomad4 FIN
AF:
0.831
Gnomad4 NFE
AF:
0.818
Gnomad4 OTH
AF:
0.729
Alfa
AF:
0.783
Hom.:
15467
Bravo
AF:
0.674
Asia WGS
AF:
0.873
AC:
3033
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxSep 13, 2019- -
Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 15, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
13
Dann
Benign
0.67

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: rs2581434; hg19: chr4-41992677; COSMIC: COSV52558106; COSMIC: COSV52558106; API