chr19-55014192-C-CGGGA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001083899.2(GP6):c.1752_1753insTCCC(p.Gly585SerfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 152,220 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0059 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00072 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
GP6
NM_001083899.2 frameshift
NM_001083899.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.268
Genes affected
GP6 (HGNC:14388): (glycoprotein VI platelet) This gene encodes a platelet membrane glycoprotein of the immunoglobulin superfamily. The encoded protein is a receptor for collagen and plays a critical role in collagen-induced platelet aggregation and thrombus formation. The encoded protein forms a complex with the Fc receptor gamma-chain that initiates the platelet activation signaling cascade upon collagen binding. Mutations in this gene are a cause of platelet-type bleeding disorder-11 (BDPLT11). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 19-55014192-C-CGGGA is Benign according to our data. Variant chr19-55014192-C-CGGGA is described in ClinVar as [Likely_benign]. Clinvar id is 777546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00592 (901/152220) while in subpopulation AFR AF= 0.0209 (870/41530). AF 95% confidence interval is 0.0198. There are 11 homozygotes in gnomad4. There are 435 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.1752_1753insTCCC | p.Gly585SerfsTer7 | frameshift_variant | 8/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+7728_121+7729insGGGA | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1752_1753insTCCC | p.Gly585SerfsTer7 | frameshift_variant | 8/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+7728_155+7729insGGGA | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00594 AC: 903AN: 152102Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00125 AC: 185AN: 147996Hom.: 1 AF XY: 0.000919 AC XY: 74AN XY: 80484
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000722 AC: 413AN: 571810Hom.: 1 Cov.: 6 AF XY: 0.000543 AC XY: 168AN XY: 309542
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Data not reliable, filtered out with message: AS_VQSR
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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
GP6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at