19-55027704-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001083899.2(GP6):​c.484A>C​(p.Arg162Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 1,611,948 control chromosomes in the GnomAD database, including 570,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 53186 hom., cov: 33)
Exomes 𝑓: 0.84 ( 517130 hom. )

Consequence

GP6
NM_001083899.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.191
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 19-55027704-T-G is Benign according to our data. Variant chr19-55027704-T-G is described in ClinVar as [Benign]. Clinvar id is 257418.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-55027704-T-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GP6NM_001083899.2 linkc.484A>C p.Arg162Arg synonymous_variant Exon 4 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.484A>C p.Arg162Arg synonymous_variant Exon 4 of 8 1 NM_001083899.2 ENSP00000308782.3 Q9HCN6-3
GP6ENST00000417454.5 linkc.484A>C p.Arg162Arg synonymous_variant Exon 4 of 8 1 ENSP00000394922.1 Q9HCN6-1

Frequencies

GnomAD3 genomes
AF:
0.834
AC:
126867
AN:
152070
Hom.:
53160
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.773
Gnomad AMI
AF:
0.770
Gnomad AMR
AF:
0.887
Gnomad ASJ
AF:
0.795
Gnomad EAS
AF:
0.976
Gnomad SAS
AF:
0.786
Gnomad FIN
AF:
0.890
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.846
Gnomad OTH
AF:
0.847
GnomAD3 exomes
AF:
0.853
AC:
212976
AN:
249534
Hom.:
91456
AF XY:
0.848
AC XY:
114776
AN XY:
135400
show subpopulations
Gnomad AFR exome
AF:
0.765
Gnomad AMR exome
AF:
0.927
Gnomad ASJ exome
AF:
0.800
Gnomad EAS exome
AF:
0.983
Gnomad SAS exome
AF:
0.787
Gnomad FIN exome
AF:
0.884
Gnomad NFE exome
AF:
0.840
Gnomad OTH exome
AF:
0.843
GnomAD4 exome
AF:
0.841
AC:
1227329
AN:
1459760
Hom.:
517130
Cov.:
43
AF XY:
0.840
AC XY:
609910
AN XY:
726298
show subpopulations
Gnomad4 AFR exome
AF:
0.764
Gnomad4 AMR exome
AF:
0.923
Gnomad4 ASJ exome
AF:
0.795
Gnomad4 EAS exome
AF:
0.981
Gnomad4 SAS exome
AF:
0.789
Gnomad4 FIN exome
AF:
0.883
Gnomad4 NFE exome
AF:
0.838
Gnomad4 OTH exome
AF:
0.839
GnomAD4 genome
AF:
0.834
AC:
126953
AN:
152188
Hom.:
53186
Cov.:
33
AF XY:
0.838
AC XY:
62397
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.773
Gnomad4 AMR
AF:
0.887
Gnomad4 ASJ
AF:
0.795
Gnomad4 EAS
AF:
0.976
Gnomad4 SAS
AF:
0.786
Gnomad4 FIN
AF:
0.890
Gnomad4 NFE
AF:
0.846
Gnomad4 OTH
AF:
0.846
Alfa
AF:
0.833
Hom.:
32464
Bravo
AF:
0.832
Asia WGS
AF:
0.885
AC:
3077
AN:
3478
EpiCase
AF:
0.839
EpiControl
AF:
0.841

ClinVar

Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Platelet-type bleeding disorder 11 Benign:1
Aug 10, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.3
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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: rs892090; hg19: chr19-55539072; API