rs12610286

Variant names:

• chr19-55030031-A-G
• rs12610286
• NM_016363.5:c.325+2108T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016363.5(GP6):​c.325+2108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,036 control chromosomes in the GnomAD database, including 8,278 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 0.32 (8278 hom., cov: 32)
• Consequence: GP6 NM_016363.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 11 publications found

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]

ENSG00000267149 (HGNC:):

GP6-AS1 (HGNC:55305): (GP6 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016363.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GP6	NM_016363.5	MANE Select	c.325+2108T>C		intron	N/A	NP_057447.5	Q9HCN6-1
	GP6	NM_001083899.2		c.325+2108T>C		intron	N/A	NP_001077368.2	Q9HCN6-3
	GP6	NM_001256017.2		c.325+2108T>C		intron	N/A	NP_001242946.2	Q9HCN6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GP6	ENST00000417454.5	TSL:1 MANE Select	c.325+2108T>C		intron	N/A	ENSP00000394922.1	Q9HCN6-1
	GP6	ENST00000310373.7	TSL:1	c.325+2108T>C		intron	N/A	ENSP00000308782.3	Q9HCN6-3
	GP6	ENST00000333884.2	TSL:1	c.325+2108T>C		intron	N/A	ENSP00000334552.2	Q9HCN6-2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49320 AN: 151918 Hom.: 8271 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.325 AC: 49356 AN: 152036 Hom.: 8278 Cov.: 32 AF XY: 0.328 AC XY: 24353 AN XY: 74322

African (AFR) AF: 0.371 AC: 15379 AN: 41448

American (AMR) AF: 0.305 AC: 4658 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2887 AN: 5160

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3050 AN: 10582

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19177 AN: 67982

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.303 Hom.: 28126

Bravo AF: 0.329

Asia WGS AF: 0.409 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12610286; hg19: chr19-55541399;