chr6-32191414-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001276501.2(GPSM3):c.435G>A(p.Gly145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,593,600 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 10 hom., cov: 31)
Exomes 𝑓: 0.0048 ( 72 hom. )
Consequence
GPSM3
NM_001276501.2 synonymous
NM_001276501.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.889
Genes affected
GPSM3 (HGNC:13945): (G protein signaling modulator 3) Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of inflammatory response. Predicted to act upstream of or within positive regulation of cytokine production involved in inflammatory response and positive regulation of leukocyte chemotaxis. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 6-32191414-C-T is Benign according to our data. Variant chr6-32191414-C-T is described in ClinVar as [Benign]. Clinvar id is 770360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.889 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00481 (6938/1441414) while in subpopulation MID AF= 0.0165 (94/5698). AF 95% confidence interval is 0.0151. There are 72 homozygotes in gnomad4_exome. There are 3784 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPSM3 | NM_001276501.2 | c.435G>A | p.Gly145= | synonymous_variant | 4/4 | ENST00000375040.8 | NP_001263430.1 | |
GPSM3 | NM_022107.3 | c.435G>A | p.Gly145= | synonymous_variant | 8/8 | NP_071390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPSM3 | ENST00000375040.8 | c.435G>A | p.Gly145= | synonymous_variant | 4/4 | 1 | NM_001276501.2 | ENSP00000364180 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00472 AC: 718AN: 152068Hom.: 10 Cov.: 31
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GnomAD3 exomes AF: 0.00657 AC: 1543AN: 234894Hom.: 17 AF XY: 0.00707 AC XY: 905AN XY: 127938
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GnomAD4 exome AF: 0.00481 AC: 6938AN: 1441414Hom.: 72 Cov.: 31 AF XY: 0.00528 AC XY: 3784AN XY: 716870
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GnomAD4 genome AF: 0.00474 AC: 722AN: 152186Hom.: 10 Cov.: 31 AF XY: 0.00464 AC XY: 345AN XY: 74406
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 25, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at