NM_001080426.3:c.205+763A>G

Variant names:

• chr1-167114567-A-G
• rs950302
• NM_001080426.3:c.205+763A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 6 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080426.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STYXL2	NM_001080426.3	MANE Select	c.205+763A>G		intron	N/A	NP_001073895.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STYXL2	ENST00000361200.7	TSL:5 MANE Select	c.205+763A>G		intron	N/A	ENSP00000354483.2
	STYXL2	ENST00000271385.9	TSL:1	c.205+763A>G		intron	N/A	ENSP00000271385.5
	STYXL2	ENST00000443333.1	TSL:5	c.205+763A>G		intron	N/A	ENSP00000404874.1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70803 AN: 151598 Hom.: 16805 Cov.: 30

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.66
PhyloP100		0.088
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs950302; hg19: chr1-167083804;