rs726117

Variant names:

• chr2-47145286-G-A
• rs726117
• NM_001163561.2:c.399+5972C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000273269 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STPG4	NM_001163561.2	c.399+5972C>T		intron_variant	Intron 3 of 6	ENST00000445927.7	NP_001157033.1
STPG4	NM_173649.3	c.399+5972C>T		intron_variant	Intron 3 of 4		NP_775920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG4	ENST00000445927.7	c.399+5972C>T		intron_variant	Intron 3 of 6	5	NM_001163561.2	ENSP00000408527.2
STPG4	ENST00000294947.2	c.399+5972C>T		intron_variant	Intron 3 of 4	1		ENSP00000294947.2
ENSG00000273269	ENST00000422269.1	n.*289+5972C>T		intron_variant	Intron 4 of 8	2		ENSP00000476793.1
STPG4	ENST00000449846.5	c.36+5972C>T		intron_variant	Intron 1 of 4	3		ENSP00000414210.1

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

African (AFR) AF: 0.293 AC: 12158 AN: 41472

American (AMR) AF: 0.463 AC: 7056 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3472

East Asian (EAS) AF: 0.716 AC: 3698 AN: 5166

South Asian (SAS) AF: 0.552 AC: 2653 AN: 4806

European-Finnish (FIN) AF: 0.486 AC: 5120 AN: 10544

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32320 AN: 67948

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.464 Hom.: 57019

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
PhyloP100		1.1
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: rs726117; hg19: chr2-47372425;