NM_001083899.2:c.664+1152T>C

Variant names:

• chr19-55024066-A-G
• rs11084382
• NM_016363.5:c.664+1152T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 7 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]

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083899.2. 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.664+1152T>C		intron	N/A	NP_057447.5	Q9HCN6-1
	GP6	NM_001083899.2		c.664+1152T>C		intron	N/A	NP_001077368.2	Q9HCN6-3
	GP6	NM_001256017.2		c.610+3512T>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.664+1152T>C		intron	N/A	ENSP00000394922.1	Q9HCN6-1
	GP6	ENST00000310373.7	TSL:1	c.664+1152T>C		intron	N/A	ENSP00000308782.3	Q9HCN6-3
	GP6	ENST00000333884.2	TSL:1	c.610+3512T>C		intron	N/A	ENSP00000334552.2	Q9HCN6-2

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111544 AN: 151782 Hom.: 41551 Cov.: 32

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

African (AFR) AF: 0.592 AC: 24488 AN: 41382

American (AMR) AF: 0.774 AC: 11812 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3466

East Asian (EAS) AF: 0.821 AC: 4236 AN: 5162

South Asian (SAS) AF: 0.706 AC: 3404 AN: 4824

European-Finnish (FIN) AF: 0.832 AC: 8786 AN: 10564

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53803 AN: 67922

Other (OTH) AF: 0.758 AC: 1599 AN: 2110

Alfa AF: 0.760 Hom.: 7489

Bravo AF: 0.724

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.54
PhyloP100		0.12
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: rs11084382; hg19: chr19-55535434;