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GeneBe

4-42020447-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_006345.4(SLC30A9):c.366C>A(p.Gly122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,577,220 control chromosomes in the GnomAD database, including 470,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.65 ( 36007 hom., cov: 32)
Exomes 𝑓: 0.77 ( 434244 hom. )

Consequence

SLC30A9
NM_006345.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.19
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 -13 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=-0.33).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-42020447-C-A is Benign according to our data. Variant chr4-42020447-C-A is described in ClinVar as [Benign]. Clinvar id is 1333133.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=2.19 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 = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC30A9NM_006345.4 linkuse as main transcriptc.366C>A p.Gly122= synonymous_variant 4/18 ENST00000264451.12
SLC30A9XM_047449525.1 linkuse as main transcriptc.366C>A p.Gly122= synonymous_variant 4/13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC30A9ENST00000264451.12 linkuse as main transcriptc.366C>A p.Gly122= synonymous_variant 4/181 NM_006345.4 P1
SLC30A9ENST00000510460.1 linkuse as main transcriptn.491C>A non_coding_transcript_exon_variant 4/42
SLC30A9ENST00000513699.5 linkuse as main transcriptc.*123C>A 3_prime_UTR_variant, NMD_transcript_variant 5/192

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.647
AC:
98325
AN:
151920
Hom.:
35995
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.275
Gnomad AMI
AF:
0.914
Gnomad AMR
AF:
0.767
Gnomad ASJ
AF:
0.710
Gnomad EAS
AF:
0.963
Gnomad SAS
AF:
0.796
Gnomad FIN
AF:
0.824
Gnomad MID
AF:
0.693
Gnomad NFE
AF:
0.777
Gnomad OTH
AF:
0.669
GnomAD3 exomes
AF:
0.768
AC:
189657
AN:
246934
Hom.:
75614
AF XY:
0.775
AC XY:
103534
AN XY:
133524
show subpopulations
Gnomad AFR exome
AF:
0.259
Gnomad AMR exome
AF:
0.828
Gnomad ASJ exome
AF:
0.711
Gnomad EAS exome
AF:
0.969
Gnomad SAS exome
AF:
0.796
Gnomad FIN exome
AF:
0.820
Gnomad NFE exome
AF:
0.779
Gnomad OTH exome
AF:
0.771
GnomAD4 exome
AF:
0.775
AC:
1103934
AN:
1425182
Hom.:
434244
Cov.:
25
AF XY:
0.776
AC XY:
551626
AN XY:
711252
show subpopulations
Gnomad4 AFR exome
AF:
0.257
Gnomad4 AMR exome
AF:
0.821
Gnomad4 ASJ exome
AF:
0.713
Gnomad4 EAS exome
AF:
0.969
Gnomad4 SAS exome
AF:
0.799
Gnomad4 FIN exome
AF:
0.816
Gnomad4 NFE exome
AF:
0.781
Gnomad4 OTH exome
AF:
0.750
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.647
AC:
98368
AN:
152038
Hom.:
36007
Cov.:
32
AF XY:
0.655
AC XY:
48704
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.768
Gnomad4 ASJ
AF:
0.710
Gnomad4 EAS
AF:
0.963
Gnomad4 SAS
AF:
0.796
Gnomad4 FIN
AF:
0.824
Gnomad4 NFE
AF:
0.777
Gnomad4 OTH
AF:
0.673
Alfa
AF:
0.746
Hom.:
65669
Bravo
AF:
0.630
Asia WGS
AF:
0.844
AC:
2923
AN:
3468

ClinVar

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

Submissions by phenotype

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
-0.33
Cadd
Benign
8.6
Dann
Benign
0.71

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: rs15857; hg19: chr4-42022464; API