rs78336249

Positions:

chr3-149162256-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000296051.7(HPS3):c.2215G>A(p.Gly739Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0145 in 1,613,918 control chromosomes in the GnomAD database, including 223 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 15 hom., cov: 33)

Exomes 𝑓: 0.015 ( 208 hom. )

Consequence

HPS3
ENST00000296051.7 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 5.81

Variant links:

Genes affected

HPS3 (HGNC:15597): (HPS3 biogenesis of lysosomal organelles complex 2 subunit 1) This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015]

HPS3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009357303).

BP6

Variant 3-149162256-G-A is Benign according to our data. Variant chr3-149162256-G-A is described in ClinVar as [Benign]. Clinvar id is 226654.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0101 (1545/152270) while in subpopulation NFE AF= 0.0167 (1135/68030). AF 95% confidence interval is 0.0159. There are 15 homozygotes in gnomad4. There are 707 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HPS3	NM_032383.5 linkuse as main transcript	c.2215G>A	p.Gly739Arg	missense_variant	12/17	ENST00000296051.7	NP_115759.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HPS3	ENST00000296051.7 linkuse as main transcript	c.2215G>A	p.Gly739Arg	missense_variant	12/17	1	NM_032383.5	ENSP00000296051	P1	Q969F9-1
HPS3	ENST00000460120.5 linkuse as main transcript	c.1720G>A	p.Gly574Arg	missense_variant	11/16	2		ENSP00000418230
HPS3	ENST00000460822.1 linkuse as main transcript	c.343G>A	p.Gly115Arg	missense_variant, NMD_transcript_variant	2/8	2		ENSP00000419824

Frequencies

GnomAD3 genomes

AF:

0.0102

AC:

1545

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00282

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00845

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0124

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0167

Gnomad OTH

AF:

0.00958

GnomAD3 exomes

AF:

0.00967

AC:

2428

AN:

251124

Hom.:

AF XY:

0.00903

AC XY:

1226

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.00308

Gnomad AMR exome

AF:

0.00655

Gnomad ASJ exome

AF:

0.00318

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00111

Gnomad FIN exome

AF:

0.0125

Gnomad NFE exome

AF:

0.0154

Gnomad OTH exome

AF:

0.0113

GnomAD4 exome

AF:

0.0149

AC:

21822

AN:

1461648

Hom.:

208

Cov.:

AF XY:

0.0145

AC XY:

10568

AN XY:

727144

show subpopulations

Gnomad4 AFR exome

AF:

0.00230

Gnomad4 AMR exome

AF:

0.00683

Gnomad4 ASJ exome

AF:

0.00310

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00115

Gnomad4 FIN exome

AF:

0.0129

Gnomad4 NFE exome

AF:

0.0178

Gnomad4 OTH exome

AF:

0.0126

GnomAD4 genome

AF:

0.0101

AC:

1545

AN:

152270

Hom.:

Cov.:

AF XY:

0.00950

AC XY:

707

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00282

Gnomad4 AMR

AF:

0.00843

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0124

Gnomad4 NFE

AF:

0.0167

Gnomad4 OTH

AF:

0.00948

Alfa

AF:

0.0136

Hom.:

Bravo

AF:

0.00949

TwinsUK

AF:

0.0178

AC:

ALSPAC

AF:

0.0192

AC:

ESP6500AA

AF:

0.00454

AC:

ESP6500EA

AF:

0.0157

AC:

135

ExAC

AF:

0.00955

AC:

1159

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.0142

EpiControl

AF:

0.0136

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Feb 21, 2013

Gly739Arg in exon 12 of HPS3: This variant is not expected to have clinical sign ificance because it has been identified in 1.6% (135/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs78336249). -

Hermansky-Pudlak syndrome 3

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. -

Hermansky-Pudlak syndrome

Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Nov 11, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.37

T;T

Eigen

Benign

0.13

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.80

T;T

MetaRNN

Benign

0.0094

T;T

MetaSVM

Benign

-0.73

MutationAssessor

Benign

0.95

L;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.48

PROVEAN

Uncertain

-2.5

N;D

REVEL

Benign

0.25

Sift

Benign

0.035

D;T

Sift4G

Uncertain

0.0050

D;D

Polyphen

0.32

B;P

Vest4

0.37

MutPred

0.65

Gain of solvent accessibility (P = 0.019);.;

MVP

0.85

MPC

0.15

ClinPred

0.018

GERP RS

5.1

Varity_R

0.24

gMVP

0.70

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over