chr10-17695245-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_003473.4(STAM):c.728+4A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00986 in 1,611,386 control chromosomes in the GnomAD database, including 108 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0074 ( 7 hom., cov: 33)
Exomes 𝑓: 0.010 ( 101 hom. )
Consequence
STAM
NM_003473.4 splice_donor_region, intron
NM_003473.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.7880
2
Clinical Significance
Conservation
PhyloP100: 1.26
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 10-17695245-A-G is Benign according to our data. Variant chr10-17695245-A-G is described in ClinVar as [Benign]. Clinvar id is 782149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAM | NM_003473.4 | c.728+4A>G | splice_donor_region_variant, intron_variant | ENST00000377524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAM | ENST00000377524.8 | c.728+4A>G | splice_donor_region_variant, intron_variant | 1 | NM_003473.4 | P1 | |||
STAM | ENST00000377500.1 | c.395+4A>G | splice_donor_region_variant, intron_variant | 5 | |||||
STAM | ENST00000494250.1 | n.316+4A>G | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00736 AC: 1120AN: 152188Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.00639 AC: 1594AN: 249606Hom.: 10 AF XY: 0.00627 AC XY: 846AN XY: 134940
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GnomAD4 exome AF: 0.0101 AC: 14769AN: 1459080Hom.: 101 Cov.: 29 AF XY: 0.00984 AC XY: 7144AN XY: 725654
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GnomAD4 genome AF: 0.00735 AC: 1120AN: 152306Hom.: 7 Cov.: 33 AF XY: 0.00700 AC XY: 521AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | STAM: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at