chr14-52750005-G-C

Variant names:

• chr14-52750005-G-C
• rs722290
• NM_145251.4:c.145-678G>C

Variant summary

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

The NM_145251.4(STYX):​c.145-678G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,004 control chromosomes in the GnomAD database, including 18,265 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 0.49 (18265 hom., cov: 32)
• Consequence: STYX NM_145251.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 15 publications found

Genes affected

STYX (HGNC:11447): (serine/threonine/tyrosine interacting protein) The protein encoded by this gene is a pseudophosphatase, able to bind potential substrates but lacking an active catalytic loop. The encoded protein may be involved in spermiogenesis. Two transcript variants encoding the same protein have been found for these genes. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STYX	NM_145251.4	c.145-678G>C		intron_variant	Intron 3 of 10	ENST00000354586.5	NP_660294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STYX	ENST00000354586.5	c.145-678G>C		intron_variant	Intron 3 of 10	1	NM_145251.4	ENSP00000346599.4
STYX	ENST00000442123.6	c.145-678G>C		intron_variant	Intron 4 of 11	1		ENSP00000403214.2
STYX	ENST00000556861.1	n.119+18293G>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74208 AN: 151886 Hom.: 18238 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.489 AC: 74288 AN: 152004 Hom.: 18265 Cov.: 32 AF XY: 0.495 AC XY: 36773 AN XY: 74282

African (AFR) AF: 0.455 AC: 18842 AN: 41436

American (AMR) AF: 0.470 AC: 7180 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1610 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2626 AN: 5178

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6389 AN: 10562

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33414 AN: 67952

Other (OTH) AF: 0.477 AC: 1007 AN: 2110

Alfa AF: 0.369 Hom.: 982

Bravo AF: 0.475

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.34
PhyloP100		-2.3
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: rs722290; hg19: chr14-53216723;