Variant chr2-232407743-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The ENST00000295453.8(ALPG):c.450C>T(p.Ser150=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00446 in 1,613,756 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0091 ( 23 hom., cov: 32)

Exomes 𝑓: 0.0040 ( 60 hom. )

Consequence

ALPG
ENST00000295453.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -6.22

Variant links:

Genes affected

ALPG (HGNC:441): (alkaline phosphatase, germ cell) There are at least four distinct but related alkaline phosphatases: intestinal, placental, placental-like, and liver/bone/kidney (tissue non-specific). The product of this gene is a membrane bound glycosylated enzyme, localized to testis, thymus and certain germ cell tumors, that is closely related to both the placental and intestinal forms of alkaline phosphatase. [provided by RefSeq, Jul 2008]

ALPG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 2-232407743-C-T is Benign according to our data. Variant chr2-232407743-C-T is described in ClinVar as [Benign]. Clinvar id is 774600.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-6.22 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00915 (1393/152266) while in subpopulation AFR AF= 0.0228 (948/41562). AF 95% confidence interval is 0.0216. There are 23 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 23 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALPG	NM_031313.3 linkuse as main transcript	c.450C>T	p.Ser150=	synonymous_variant	4/11	ENST00000295453.8	NP_112603.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALPG	ENST00000295453.8 linkuse as main transcript	c.450C>T	p.Ser150=	synonymous_variant	4/11	1	NM_031313.3	ENSP00000295453	P1

Frequencies

GnomAD3 genomes

AF:

0.00915

AC:

1392

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0229

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00864

Gnomad ASJ

AF:

0.0147

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00645

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00309

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00465

AC:

1164

AN:

250428

Hom.:

AF XY:

0.00418

AC XY:

566

AN XY:

135562

show subpopulations

Gnomad AFR exome

AF:

0.0244

Gnomad AMR exome

AF:

0.00269

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00511

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00305

Gnomad OTH exome

AF:

0.00426

GnomAD4 exome

AF:

0.00397

AC:

5799

AN:

1461490

Hom.:

Cov.:

AF XY:

0.00397

AC XY:

2889

AN XY:

727002

show subpopulations

Gnomad4 AFR exome

AF:

0.0241

Gnomad4 AMR exome

AF:

0.00257

Gnomad4 ASJ exome

AF:

0.0140

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00566

Gnomad4 FIN exome

AF:

0.000715

Gnomad4 NFE exome

AF:

0.00332

Gnomad4 OTH exome

AF:

0.00457

GnomAD4 genome

AF:

0.00915

AC:

1393

AN:

152266

Hom.:

Cov.:

AF XY:

0.00839

AC XY:

625

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0228

Gnomad4 AMR

AF:

0.00863

Gnomad4 ASJ

AF:

0.0147

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00646

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00309

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00699

Hom.:

Bravo

AF:

0.0104

Asia WGS

AF:

0.00231

AC:

AN:

3476

EpiCase

AF:

0.00425

EpiControl

AF:

0.00391

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 04, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.078

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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