rs545809

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001199013.2(STPG1):c.738-3233A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,548,420 control chromosomes in the GnomAD database, including 58,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5291 hom., cov: 32)

Exomes 𝑓: 0.27 ( 52939 hom. )

Consequence

STPG1
NM_001199013.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.294

Publications

19 publications found

Variant links:

Genes affected

STPG1 (HGNC:28070): (sperm tail PG-rich repeat containing 1) Involved in positive regulation of apoptotic process and positive regulation of mitochondrial membrane permeability involved in apoptotic process. Predicted to be located in mitochondrion and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

STPG1 links:

GRHL3 (HGNC:25839): (grainyhead like transcription factor 3) This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]

GRHL3 Gene-Disease associations (from GenCC):

van der Woude syndrome 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
van der Woude syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

GRHL3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016256869).

BP6

Variant 1-24364274-T-A is Benign according to our data. Variant chr1-24364274-T-A is described in ClinVar as Benign. ClinVar VariationId is 1164479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STPG1	NM_001199013.2 link	c.738-3233A>T		intron_variant	Intron 7 of 8	ENST00000337248.9	NP_001185942.1	Q5TH74-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG1	ENST00000337248.9 link	c.738-3233A>T		intron_variant	Intron 7 of 8	5	NM_001199013.2	ENSP00000337461.4		Q5TH74-1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39679

AN:

151960

Hom.:

5281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.299

GnomAD2 exomes

AF:

0.292

AC:

42937

AN:

147140

AF XY:

0.298

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.301

Gnomad EAS exome

AF:

0.413

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.269

Gnomad OTH exome

AF:

0.280

GnomAD4 exome

AF:

0.272

AC:

379220

AN:

1396342

Hom.:

52939

Cov.:

AF XY:

0.275

AC XY:

189187

AN XY:

688648

show subpopulations

African (AFR)

AF:

0.224

AC:

7050

AN:

31532

American (AMR)

AF:

0.288

AC:

10199

AN:

35446

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

7625

AN:

25152

East Asian (EAS)

AF:

0.413

AC:

14688

AN:

35524

South Asian (SAS)

AF:

0.368

AC:

28984

AN:

78684

European-Finnish (FIN)

AF:

0.221

AC:

10651

AN:

48150

Middle Eastern (MID)

AF:

0.358

AC:

2041

AN:

5694

European-Non Finnish (NFE)

AF:

0.261

AC:

281889

AN:

1078256

Other (OTH)

AF:

0.278

AC:

16093

AN:

57904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

17671

35342

53012

70683

88354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9726

19452

29178

38904

48630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.261

AC:

39725

AN:

152078

Hom.:

5291

Cov.:

AF XY:

0.263

AC XY:

19519

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.226

AC:

9377

AN:

41486

American (AMR)

AF:

0.256

AC:

3912

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1070

AN:

3470

East Asian (EAS)

AF:

0.402

AC:

2069

AN:

5144

South Asian (SAS)

AF:

0.367

AC:

1768

AN:

4814

European-Finnish (FIN)

AF:

0.225

AC:

2377

AN:

10584

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.268

AC:

18211

AN:

67972

Other (OTH)

AF:

0.298

AC:

630

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1521

3042

4562

6083

7604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.276

Hom.:

4533

Bravo

AF:

0.261

TwinsUK

AF:

0.273

AC:

1011

ALSPAC

AF:

0.274

AC:

1055

ExAC

AF:

0.275

AC:

5754

Asia WGS

AF:

0.359

AC:

1248

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Van der Woude syndrome 2

Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.4

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.27

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.048

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.2

PhyloP100

-0.29

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.6

REVEL

Benign

0.026

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Vest4

0.096

MPC

0.60

ClinPred

0.023

GERP RS

-1.2

Varity_R

0.64

gMVP

0.46

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over