rs11084382

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001083899.2(GP6):​c.664+1152T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 151,900 control chromosomes in the GnomAD database, including 41,560 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 41560 hom., cov: 32)

Consequence

GP6
NM_001083899.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121
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.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GP6NM_001083899.2 linkc.664+1152T>C intron_variant ENST00000310373.7 NP_001077368.2 Q9HCN6-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GP6ENST00000310373.7 linkc.664+1152T>C intron_variant 1 NM_001083899.2 ENSP00000308782.3 Q9HCN6-3
GP6ENST00000417454.5 linkc.664+1152T>C intron_variant 1 ENSP00000394922.1 Q9HCN6-1

Frequencies

GnomAD3 genomes
AF:
0.735
AC:
111544
AN:
151782
Hom.:
41551
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.592
Gnomad AMI
AF:
0.741
Gnomad AMR
AF:
0.773
Gnomad ASJ
AF:
0.737
Gnomad EAS
AF:
0.822
Gnomad SAS
AF:
0.706
Gnomad FIN
AF:
0.832
Gnomad MID
AF:
0.825
Gnomad NFE
AF:
0.792
Gnomad OTH
AF:
0.761
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.735
AC:
111598
AN:
151900
Hom.:
41560
Cov.:
32
AF XY:
0.739
AC XY:
54849
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.592
Gnomad4 AMR
AF:
0.774
Gnomad4 ASJ
AF:
0.737
Gnomad4 EAS
AF:
0.821
Gnomad4 SAS
AF:
0.706
Gnomad4 FIN
AF:
0.832
Gnomad4 NFE
AF:
0.792
Gnomad4 OTH
AF:
0.758
Alfa
AF:
0.765
Hom.:
7344
Bravo
AF:
0.724
Asia WGS
AF:
0.730
AC:
2540
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
6.9
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs11084382; hg19: chr19-55535434; API