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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.173
Variant links:
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]
GP6-AS1 (HGNC:55305): (GP6 antisense RNA 1)

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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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GP6NM_001083899.2 linkc.1206_1209dupTCTG p.Pro404SerfsTer61 frameshift_variant Exon 8 of 8 ENST00000310373.7 NP_001077368.2 Q9HCN6-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GP6ENST00000310373.7 linkc.1206_1209dupTCTG p.Pro404SerfsTer61 frameshift_variant Exon 8 of 8 1 NM_001083899.2 ENSP00000308782.3 Q9HCN6-3
GP6ENST00000417454 linkc.*182_*185dupTCTG 3_prime_UTR_variant Exon 8 of 8 1 ENSP00000394922.1 Q9HCN6-1

Frequencies

GnomAD3 genomes
AF:
0.0469
AC:
7123
AN:
151980
Hom.:
291
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0784
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0786
Gnomad ASJ
AF:
0.0135
Gnomad EAS
AF:
0.148
Gnomad SAS
AF:
0.0651
Gnomad FIN
AF:
0.0155
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0194
Gnomad OTH
AF:
0.0350
GnomAD3 exomes
AF:
0.0467
AC:
11550
AN:
247204
Hom.:
434
AF XY:
0.0439
AC XY:
5883
AN XY:
134012
show subpopulations
Gnomad AFR exome
AF:
0.0784
Gnomad AMR exome
AF:
0.0907
Gnomad ASJ exome
AF:
0.0124
Gnomad EAS exome
AF:
0.145
Gnomad SAS exome
AF:
0.0604
Gnomad FIN exome
AF:
0.0142
Gnomad NFE exome
AF:
0.0197
Gnomad OTH exome
AF:
0.0327
GnomAD4 exome
AF:
0.0308
AC:
44944
AN:
1461370
Hom.:
1345
Cov.:
39
AF XY:
0.0309
AC XY:
22465
AN XY:
726974
show subpopulations
Gnomad4 AFR exome
AF:
0.0816
Gnomad4 AMR exome
AF:
0.0892
Gnomad4 ASJ exome
AF:
0.0117
Gnomad4 EAS exome
AF:
0.172
Gnomad4 SAS exome
AF:
0.0585
Gnomad4 FIN exome
AF:
0.0138
Gnomad4 NFE exome
AF:
0.0208
Gnomad4 OTH exome
AF:
0.0350
GnomAD4 genome
AF:
0.0469
AC:
7137
AN:
152098
Hom.:
291
Cov.:
31
AF XY:
0.0474
AC XY:
3526
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.0783
Gnomad4 AMR
AF:
0.0787
Gnomad4 ASJ
AF:
0.0135
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.0649
Gnomad4 FIN
AF:
0.0155
Gnomad4 NFE
AF:
0.0194
Gnomad4 OTH
AF:
0.0374

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 submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 03, 2025- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs768134535; hg19: chr19-55526103; API