1-21568242-T-C

Position:

chr1-21568242-T-C

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1

The NM_000478.6(ALPL):c.787T>C(p.Tyr263His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,613,726 control chromosomes in the GnomAD database, including 21,866 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. Y263Y) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.18 ( 3121 hom., cov: 31)

Exomes 𝑓: 0.14 ( 18745 hom. )

Consequence

ALPL
NM_000478.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:15O:1

Conservation

PhyloP100: 0.0570

Variant links:

Genes affected

ALPL (HGNC:438): (alkaline phosphatase, biomineralization associated) This gene encodes a member of the alkaline phosphatase family of proteins. There are at least four distinct but related alkaline phosphatases: intestinal, placental, placental-like, and liver/bone/kidney (tissue non-specific). The first three are located together on chromosome 2, while the tissue non-specific form is located on chromosome 1. The product of this gene is a membrane bound glycosylated enzyme that is not expressed in any particular tissue and is, therefore, referred to as the tissue-nonspecific form of the enzyme. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature enzyme. This enzyme may play a role in bone mineralization. Mutations in this gene have been linked to hypophosphatasia, a disorder that is characterized by hypercalcemia and skeletal defects. [provided by RefSeq, Oct 2015]

ALPL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_000478.6

BP4

Computational evidence support a benign effect (MetaRNN=0.0024879575).

BP6

Variant 1-21568242-T-C is Benign according to our data. Variant chr1-21568242-T-C is described in ClinVar as [Benign]. Clinvar id is 198423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-21568242-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALPL	NM_000478.6 linkuse as main transcript	c.787T>C	p.Tyr263His	missense_variant	7/12	ENST00000374840.8	NP_000469.3	P05186-1A0A024RAB4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ALPL	ENST00000374840.8 linkuse as main transcript	c.787T>C	p.Tyr263His	missense_variant	7/12	1	NM_000478.6	ENSP00000363973.3	P05186-1
ALPL	ENST00000374832.5 linkuse as main transcript	c.787T>C	p.Tyr263His	missense_variant	7/12	2		ENSP00000363965.1	P05186-1
ALPL	ENST00000540617.5 linkuse as main transcript	c.622T>C	p.Tyr208His	missense_variant	6/11	2		ENSP00000442672.1	P05186-3
ALPL	ENST00000539907.5 linkuse as main transcript	c.556T>C	p.Tyr186His	missense_variant	5/10	2		ENSP00000437674.1	P05186-2

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27756

AN:

151812

Hom.:

3108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.118

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.183

AC:

46072

AN:

251140

Hom.:

5476

AF XY:

0.178

AC XY:

24224

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.256

Gnomad AMR exome

AF:

0.251

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.445

Gnomad SAS exome

AF:

0.216

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.107

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.140

AC:

205273

AN:

1461796

Hom.:

18745

Cov.:

AF XY:

0.141

AC XY:

102884

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.265

Gnomad4 AMR exome

AF:

0.246

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.511

Gnomad4 SAS exome

AF:

0.217

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.183

AC:

27806

AN:

151930

Hom.:

3121

Cov.:

AF XY:

0.191

AC XY:

14155

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.252

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.453

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.135

Hom.:

3027

Bravo

AF:

0.190

TwinsUK

AF:

0.105

AC:

388

ALSPAC

AF:

0.113

AC:

434

ESP6500AA

AF:

0.252

AC:

1109

ESP6500EA

AF:

0.111

AC:

956

ExAC

AF:

0.179

AC:

21693

Asia WGS

AF:

0.327

AC:

1135

AN:

3478

EpiCase

AF:

0.108

EpiControl

AF:

0.110

ClinVar

Significance: Benign

Submissions summary: Benign:15Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 14, 2014	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2018	This variant is associated with the following publications: (PMID: 32160374, 31600233, 19931660, 28881669, 9781036, 15824850, 18724009) -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hypophosphatasia

Benign:2Other:1

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 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. -
not provided, no classification provided	literature only	GeneReviews	-	- -

Osteogenesis imperfecta

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Jul 09, 2022

- -

Infantile hypophosphatasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Adult hypophosphatasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Childhood hypophosphatasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Benign

9.8

DANN

Benign

0.69

DEOGEN2

Uncertain

0.56

D;.;.;D

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.94

FATHMM_MKL

Benign

0.016

LIST_S2

Benign

0.071

.;T;T;T

MetaRNN

Benign

0.0025

T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-0.070

N;.;.;N

PrimateAI

Benign

0.39

PROVEAN

Benign

1.6

N;N;N;N

REVEL

Benign

0.19

Sift

Benign

1.0

T;T;T;T

Sift4G

Benign

0.59

T;T;T;T

Polyphen

0.0

B;.;.;B

Vest4

0.037

MPC

0.53

ClinPred

0.00041

GERP RS

1.9

Varity_R

0.031

gMVP

0.72

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