rs726117

Positions:

• chr2-47145286-G-A
• chr2-47145286-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001163561.2(STPG4):​c.399+5972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,964 control chromosomes in the GnomAD database, including 15,359 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 0.44 (15359 hom., cov: 32)
• Consequence: STPG4 NM_001163561.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

STPG4 (HGNC:26850): (sperm-tail PG-rich repeat containing 4) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in DNA demethylation of male pronucleus and positive regulation of DNA demethylation. Predicted to act upstream of or within C-5 methylation of cytosine. Predicted to be located in cytoplasm and nucleus. Predicted to be active in female pronucleus; germinal vesicle; and male pronucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STPG4	NM_001163561.2	c.399+5972C>T		intron_variant		ENST00000445927.7
STPG4	NM_173649.3	c.399+5972C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STPG4	ENST00000445927.7	c.399+5972C>T		intron_variant		5	NM_001163561.2	P1
STPG4	ENST00000294947.2	c.399+5972C>T		intron_variant		1
STPG4	ENST00000449846.5	c.38+5972C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66428 AN: 151846 Hom.: 15354 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.437 AC: 66448 AN: 151964 Hom.: 15359 Cov.: 32 AF XY: 0.443 AC XY: 32893 AN XY: 74266

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.476

Alfa AF: 0.475 Hom.: 36090

Bravo AF: 0.428

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs726117; hg19: chr2-47372425;