rs950302

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
STYXL2NM_001080426.3 linkuse as main transcriptc.205+763A>G intron_variant ENST00000361200.7 NP_001073895.1
STYXL2XM_011510146.3 linkuse as main transcriptc.88+763A>G intron_variant XP_011508448.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
STYXL2ENST00000361200.7 linkuse as main transcriptc.205+763A>G intron_variant 5 NM_001080426.3 ENSP00000354483 P1
STYXL2ENST00000271385.9 linkuse as main transcriptc.205+763A>G intron_variant 1 ENSP00000271385 P1
STYXL2ENST00000443333.1 linkuse as main transcriptc.205+763A>G intron_variant 5 ENSP00000404874 P1
GPA33ENST00000632571.1 linkuse as main transcriptc.-281-41028T>C intron_variant 4 ENSP00000488407

Frequencies

GnomAD3 genomes
AF:
0.467
AC:
70803
AN:
151598
Hom.:
16805
Cov.:
30
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.:
30
AF XY:
0.466
AC XY:
34571
AN XY:
74138
show subpopulations
Gnomad4 AFR
AF:
0.477
Gnomad4 AMR
AF:
0.427
Gnomad4 ASJ
AF:
0.523
Gnomad4 EAS
AF:
0.734
Gnomad4 SAS
AF:
0.406
Gnomad4 FIN
AF:
0.458
Gnomad4 NFE
AF:
0.453
Gnomad4 OTH
AF:
0.461
Alfa
AF:
0.454
Hom.:
7425
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
DANN
Benign
0.66

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.

Other links and lift over

dbSNP: rs950302; hg19: chr1-167083804; API