chr10-69103949-C-T
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.Ser102=) 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 GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGN | NM_002727.4 | c.306C>T | p.Ser102= | synonymous_variant | 3/3 | ENST00000242465.4 | |
SRGN | NM_001321053.2 | c.306C>T | p.Ser102= | synonymous_variant | 4/4 | ||
SRGN | NM_001321054.1 | c.138C>T | p.Ser46= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGN | ENST00000242465.4 | c.306C>T | p.Ser102= | synonymous_variant | 3/3 | 1 | NM_002727.4 | P1 | |
SRGN | ENST00000462445.1 | n.210C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
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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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | SRGN: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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