19-55024604-T-C

Position:

• chr19-55024604-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001083899.2(GP6):​c.664+614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,148 control chromosomes in the GnomAD database, including 3,871 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 0.22 (3871 hom., cov: 32)
• Consequence: GP6 NM_001083899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GP6	NM_001083899.2	c.664+614A>G		intron_variant		ENST00000310373.7	NP_001077368.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GP6	ENST00000310373.7	c.664+614A>G		intron_variant		1	NM_001083899.2	ENSP00000308782.3
GP6	ENST00000417454.5	c.664+614A>G		intron_variant		1		ENSP00000394922.1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33514 AN: 152030 Hom.: 3876 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.241

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33527 AN: 152148 Hom.: 3871 Cov.: 32 AF XY: 0.222 AC XY: 16543 AN XY: 74378

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.240

Alfa AF: 0.227 Hom.: 4634

Bravo AF: 0.228

Asia WGS AF: 0.260 AC: 905 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	3.2
DANN	Benign	0.27
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97

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

Other links and lift over

dbSNP: rs11669150; hg19: chr19-55535972; COSMIC: COSV59980273; COSMIC: COSV59980273;