dbSNP rs950302: STYXL2:c.205+763A>G (chr1-167114567-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080426.3(STYXL2):c.205+763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,716 control chromosomes in the GnomAD database, including 16,808 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 16808 hom., cov: 30)

Consequence

STYXL2
NM_001080426.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

Publications

6 publications found

Variant links:

Genes affected

STYXL2 (HGNC:25034): (serine/threonine/tyrosine interacting like 2) Predicted to enable protein tyrosine/serine/threonine phosphatase activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in sarcomere. [provided by Alliance of Genome Resources, Apr 2022]

STYXL2 links:

GPA33 (HGNC:4445): (glycoprotein A33) The glycoprotein encoded by this gene is a cell surface antigen that is expressed in greater than 95% of human colon cancers. The open reading frame encodes a 319-amino acid polypeptide having a putative secretory signal sequence and 3 potential glycosylation sites. The predicted mature protein has a 213-amino acid extracellular region, a single transmembrane domain, and a 62-amino acid intracellular tail. The sequence of the extracellular region contains 2 domains characteristic of the CD2 subgroup of the immunoglobulin (Ig) superfamily. [provided by RefSeq, Jul 2008]

GPA33 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STYXL2	NM_001080426.3 link	c.205+763A>G		intron_variant	Intron 3 of 5	ENST00000361200.7	NP_001073895.1
STYXL2	XM_011510146.3 link	c.88+763A>G		intron_variant	Intron 2 of 4		XP_011508448.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
STYXL2	ENST00000361200.7 link	c.205+763A>G	intron_variant	Intron 3 of 5	5	NM_001080426.3	ENSP00000354483.2
STYXL2	ENST00000271385.9 link	c.205+763A>G	intron_variant	Intron 3 of 5	1		ENSP00000271385.5
STYXL2	ENST00000443333.1 link	c.205+763A>G	intron_variant	Intron 2 of 4	5		ENSP00000404874.1
GPA33	ENST00000632571.1 link	c.-281-41028T>C	intron_variant	Intron 1 of 3	4		ENSP00000488407.1

Frequencies

GnomAD3 genomes

AF:

0.467

AC:

70803

AN:

151598

Hom.:

16805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.523

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.463

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.467

AC:

70838

AN:

151716

Hom.:

16808

Cov.:

AF XY:

0.466

AC XY:

34571

AN XY:

74138

show subpopulations

African (AFR)

AF:

0.477

AC:

19723

AN:

41334

American (AMR)

AF:

0.427

AC:

6517

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.523

AC:

1816

AN:

3472

East Asian (EAS)

AF:

0.734

AC:

3751

AN:

5112

South Asian (SAS)

AF:

0.406

AC:

1948

AN:

4794

European-Finnish (FIN)

AF:

0.458

AC:

4820

AN:

10534

Middle Eastern (MID)

AF:

0.462

AC:

135

AN:

292

European-Non Finnish (NFE)

AF:

0.453

AC:

30728

AN:

67902

Other (OTH)

AF:

0.461

AC:

971

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1876

3752

5627

7503

9379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

636

1272

1908

2544

3180

<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:

0.456

Hom.:

8330

Bravo

AF:

0.469

Asia WGS

AF:

0.569

AC:

1980

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.8

(source)

DANN

Benign

0.66

PhyloP100

0.088

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over