19-55014735-GCAGACAGA-GCAGACAGACAGA
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PVS1_StrongBP6_Very_StrongBA1
The NM_001083899.2(GP6):c.1206_1209dupTCTG(p.Pro404SerfsTer61) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 1,613,468 control chromosomes in the GnomAD database, including 1,636 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.047 ( 291 hom., cov: 31)
Exomes 𝑓: 0.031 ( 1345 hom. )
Consequence
GP6
NM_001083899.2 frameshift
NM_001083899.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.173
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 -12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.351 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BP6
Variant 19-55014735-G-GCAGA is Benign according to our data. Variant chr19-55014735-G-GCAGA is described in ClinVar as [Benign]. Clinvar id is 257410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1206_1209dupTCTG | p.Pro404SerfsTer61 | frameshift_variant | Exon 8 of 8 | 1 | NM_001083899.2 | ENSP00000308782.3 | ||
GP6 | ENST00000417454 | c.*182_*185dupTCTG | 3_prime_UTR_variant | Exon 8 of 8 | 1 | ENSP00000394922.1 |
Frequencies
GnomAD3 genomes AF: 0.0469 AC: 7123AN: 151980Hom.: 291 Cov.: 31
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GnomAD3 exomes AF: 0.0467 AC: 11550AN: 247204Hom.: 434 AF XY: 0.0439 AC XY: 5883AN XY: 134012
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GnomAD4 exome AF: 0.0308 AC: 44944AN: 1461370Hom.: 1345 Cov.: 39 AF XY: 0.0309 AC XY: 22465AN XY: 726974
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GnomAD4 genome AF: 0.0469 AC: 7137AN: 152098Hom.: 291 Cov.: 31 AF XY: 0.0474 AC XY: 3526AN XY: 74356
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at