2-47121208-C-T

Variant names:

• chr2-47121208-C-T
• rs1880583
• NM_001163561.2:c.519+8733G>A

Variant summary

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

The NM_001163561.2(STPG4):​c.519+8733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 154,038 control chromosomes in the GnomAD database, including 37,455 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 0.68 (36688 hom., cov: 30)
  • Exomes 𝑓: 0.84 (767 hom.)
• Consequence: STPG4 NM_001163561.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163561.2. 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
	STPG4	NM_001163561.2	MANE Select	c.519+8733G>A		intron	N/A	NP_001157033.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG4	ENST00000445927.7	TSL:5 MANE Select	c.519+8733G>A		intron	N/A	ENSP00000408527.2
	ENSG00000273269	ENST00000422269.1	TSL:2	n.*410-55G>A		intron	N/A	ENSP00000476793.1
	STPG4	ENST00000449846.5	TSL:3	c.156+8733G>A		intron	N/A	ENSP00000414210.1

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102621 AN: 151776 Hom.: 36665 Cov.: 30

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.724

GnomAD4 exome AF: 0.840 AC: 1800 AN: 2144 Hom.: 767 AF XY: 0.824 AC XY: 888 AN XY: 1078

African (AFR) AF: 0.429 AC: 30 AN: 70

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.872 AC: 75 AN: 86

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.875 AC: 1425 AN: 1628

European-Non Finnish (NFE) AF: 0.767 AC: 138 AN: 180

Other (OTH) AF: 0.724 AC: 126 AN: 174

GnomAD4 genome AF: 0.676 AC: 102685 AN: 151894 Hom.: 36688 Cov.: 30 AF XY: 0.682 AC XY: 50650 AN XY: 74232

African (AFR) AF: 0.429 AC: 17749 AN: 41410

American (AMR) AF: 0.765 AC: 11676 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2813 AN: 3466

East Asian (EAS) AF: 0.933 AC: 4800 AN: 5146

South Asian (SAS) AF: 0.877 AC: 4214 AN: 4806

European-Finnish (FIN) AF: 0.716 AC: 7561 AN: 10554

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.755 AC: 51316 AN: 67938

Other (OTH) AF: 0.726 AC: 1530 AN: 2108

Alfa AF: 0.743 Hom.: 62540

Bravo AF: 0.667

Asia WGS AF: 0.877 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.20
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: rs1880583; hg19: chr2-47348347;