rs5030705
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000310373.7(GP6):c.507G>A(p.Thr169=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,611,158 control chromosomes in the GnomAD database, including 32,180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 2270 hom., cov: 34)
Exomes 𝑓: 0.19 ( 29910 hom. )
Consequence
GP6
ENST00000310373.7 synonymous
ENST00000310373.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.85
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 19-55027681-C-T is Benign according to our data. Variant chr19-55027681-C-T is described in ClinVar as [Benign]. Clinvar id is 257420.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.85 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.507G>A | p.Thr169= | synonymous_variant | 4/8 | ENST00000310373.7 | NP_001077368.2 | |
GP6-AS1 | XR_001754012.3 | n.122-15119C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.507G>A | p.Thr169= | synonymous_variant | 4/8 | 1 | NM_001083899.2 | ENSP00000308782 | ||
GP6-AS1 | ENST00000593060.5 | n.156-15119C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.146 AC: 22215AN: 152118Hom.: 2270 Cov.: 34
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GnomAD3 exomes AF: 0.148 AC: 36815AN: 249498Hom.: 3600 AF XY: 0.148 AC XY: 20026AN XY: 135390
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GnomAD4 exome AF: 0.192 AC: 280838AN: 1458922Hom.: 29910 Cov.: 39 AF XY: 0.189 AC XY: 137384AN XY: 726042
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GnomAD4 genome AF: 0.146 AC: 22205AN: 152236Hom.: 2270 Cov.: 34 AF XY: 0.145 AC XY: 10774AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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