3-129062280-C-T

Position:

• chr3-129062280-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000174.5(GP9):​c.*7C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00725 in 1,534,322 control chromosomes in the GnomAD database, including 301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.027 (151 hom., cov: 33)
  • Exomes 𝑓: 0.0051 (150 hom.)
• Consequence: GP9 NM_000174.5 3_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 0.250

Genes affected

GP9 (HGNC:4444): (glycoprotein IX platelet) This gene encodes a small membrane glycoprotein found on the surface of human platelets. It forms a 1-to-1 noncovalent complex with glycoprotein Ib, a platelet surface membrane glycoprotein complex that functions as a receptor for von Willebrand factor. The complete receptor complex includes noncovalent association of the alpha and beta subunits with the protein encoded by this gene and platelet glycoprotein V. Defects in this gene are a cause of Bernard-Soulier syndrome, also known as giant platelet disease. These patients have unusually large platelets and have a clinical bleeding tendency. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 3-129062280-C-T is Benign according to our data. Variant chr3-129062280-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 255470.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GP9	NM_000174.5	c.*7C>T		3_prime_UTR_variant	3/3	ENST00000307395.5
GP9	XM_047447997.1	c.*7C>T		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GP9	ENST00000307395.5	c.*7C>T		3_prime_UTR_variant	3/3	1	NM_000174.5	P1

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4093 AN: 152118 Hom.: 151 Cov.: 33

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00281

Gnomad OTH AF: 0.0292

GnomAD3 exomes AF: 0.00994 AC: 1397 AN: 140486 Hom.: 32 AF XY: 0.00837 AC XY: 639 AN XY: 76322

Gnomad AFR exome AF: 0.0841

Gnomad AMR exome AF: 0.0117

Gnomad ASJ exome AF: 0.0418

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00103

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00327

Gnomad OTH exome AF: 0.0132

GnomAD4 exome AF: 0.00509 AC: 7030 AN: 1382086 Hom.: 150 Cov.: 29 AF XY: 0.00487 AC XY: 3315 AN XY: 681206

Gnomad4 AFR exome AF: 0.0800

Gnomad4 AMR exome AF: 0.0126

Gnomad4 ASJ exome AF: 0.0435

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00112

Gnomad4 FIN exome AF: 0.0000211

Gnomad4 NFE exome AF: 0.00199

Gnomad4 OTH exome AF: 0.0121

GnomAD4 genome AF: 0.0269 AC: 4090 AN: 152236 Hom.: 151 Cov.: 33 AF XY: 0.0265 AC XY: 1974 AN XY: 74430

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.0198

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00281

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0114 Hom.: 15

Bravo AF: 0.0301

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

Bernard Soulier syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.72
DANN	Benign	0.82

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

Other links and lift over

dbSNP: rs115005114; hg19: chr3-128781123;