chr5-69116562-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_022902.5(SLC30A5):c.1241G>A(p.Ser414Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000687 in 1,456,448 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
SLC30A5
NM_022902.5 missense
NM_022902.5 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 5.22
Genes affected
SLC30A5 (HGNC:19089): (solute carrier family 30 member 5) This gene encodes a member of the SLC30A/ZnT family of zinc transporter proteins. ZnT proteins mediate both cellular zinc efflux and zinc sequestration into membrane-bound organelles. The encoded protein plays a role in the early secretory pathway as a heterodimer with zinc transporter 6, and may also regulate zinc sequestration into secretory granules of pancreatic beta cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 19. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.10035595).
BP6
?
Variant 5-69116562-G-A is Benign according to our data. Variant chr5-69116562-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2321125.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A5 | NM_022902.5 | c.1241G>A | p.Ser414Asn | missense_variant | 10/16 | ENST00000396591.8 | |
SLC30A5 | XM_005248569.4 | c.1118G>A | p.Ser373Asn | missense_variant | 9/15 | ||
SLC30A5 | XM_006714672.5 | c.1241G>A | p.Ser414Asn | missense_variant | 10/15 | ||
SLC30A5 | XM_017009749.2 | c.1118G>A | p.Ser373Asn | missense_variant | 9/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A5 | ENST00000396591.8 | c.1241G>A | p.Ser414Asn | missense_variant | 10/16 | 1 | NM_022902.5 | P1 | |
SLC30A5 | ENST00000507354.5 | n.1439G>A | non_coding_transcript_exon_variant | 7/11 | 1 | ||||
ENST00000690195.2 | n.683-1160C>T | intron_variant, non_coding_transcript_variant | |||||||
ENST00000504129.1 | n.609-1160C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244840Hom.: 0 AF XY: 0.00000755 AC XY: 1AN XY: 132370
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GnomAD4 exome AF: 0.00000687 AC: 10AN: 1456448Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 6AN XY: 724354
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GnomAD4 genome ? Cov.: 33
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?
Cov.:
33
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?
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Loss of phosphorylation at S414 (P = 0.0495);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at