chr10-17688058-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003473.4(STAM):c.329C>G(p.Ala110Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000649 in 1,603,670 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000068 ( 1 hom. )
Consequence
STAM
NM_003473.4 missense
NM_003473.4 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
STAM (HGNC:11357): (signal transducing adaptor molecule) This gene encodes a member of the signal-transducing adaptor molecule family. These proteins mediate downstream signaling of cytokine receptors and also play a role in ER to Golgi trafficking by interacting with the coat protein II complex. The encoded protein also associates with hepatocyte growth factor-regulated substrate to form the endosomal sorting complex required for transport-0 (ESCRT-0), which sorts ubiquitinated membrane proteins to the ESCRT-1 complex for lysosomal degradation. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAM | NM_003473.4 | c.329C>G | p.Ala110Gly | missense_variant | 5/14 | ENST00000377524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAM | ENST00000377524.8 | c.329C>G | p.Ala110Gly | missense_variant | 5/14 | 1 | NM_003473.4 | P1 | |
STAM | ENST00000377500.1 | c.-5C>G | 5_prime_UTR_variant | 2/6 | 5 | ||||
STAM | ENST00000486183.1 | n.175C>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
STAM | ENST00000445846.1 | c.*304C>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152100Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000490 AC: 12AN: 244966Hom.: 0 AF XY: 0.0000604 AC XY: 8AN XY: 132412
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GnomAD4 exome AF: 0.0000675 AC: 98AN: 1451452Hom.: 1 Cov.: 30 AF XY: 0.0000734 AC XY: 53AN XY: 721888
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74412
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.329C>G (p.A110G) alteration is located in exon 5 (coding exon 5) of the STAM gene. This alteration results from a C to G substitution at nucleotide position 329, causing the alanine (A) at amino acid position 110 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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