10-69103949-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_002727.4(SRGN):c.306C>T(p.Ser102Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,614,182 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0015 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 9 hom. )
Consequence
SRGN
NM_002727.4 synonymous
NM_002727.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.20
Genes affected
SRGN (HGNC:9361): (serglycin) This gene encodes a protein best known as a hematopoietic cell granule proteoglycan. Proteoglycans stored in the secretory granules of many hematopoietic cells also contain a protease-resistant peptide core, which may be important for neutralizing hydrolytic enzymes. This encoded protein was found to be associated with the macromolecular complex of granzymes and perforin, which may serve as a mediator of granule-mediated apoptosis. Two transcript variants, only one of them protein-coding, have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 10-69103949-C-T is Benign according to our data. Variant chr10-69103949-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 735160.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.2 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRGN | NM_002727.4 | c.306C>T | p.Ser102Ser | synonymous_variant | Exon 3 of 3 | ENST00000242465.4 | NP_002718.2 | |
SRGN | NM_001321053.2 | c.306C>T | p.Ser102Ser | synonymous_variant | Exon 4 of 4 | NP_001307982.1 | ||
SRGN | NM_001321054.1 | c.138C>T | p.Ser46Ser | synonymous_variant | Exon 2 of 2 | NP_001307983.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00145 AC: 221AN: 152176Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00215 AC: 540AN: 251472Hom.: 2 AF XY: 0.00278 AC XY: 378AN XY: 135914
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GnomAD4 exome AF: 0.00137 AC: 1998AN: 1461888Hom.: 9 Cov.: 30 AF XY: 0.00165 AC XY: 1199AN XY: 727248
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GnomAD4 genome AF: 0.00146 AC: 222AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.00160 AC XY: 119AN XY: 74454
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Apr 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SRGN: BP4, BP7 -
Mar 27, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at