chr2-47121208-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STPG4	NM_001163561.2	c.519+8733G>A		intron_variant	Intron 5 of 6	ENST00000445927.7	NP_001157033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG4	ENST00000445927.7	c.519+8733G>A		intron_variant	Intron 5 of 6	5	NM_001163561.2	ENSP00000408527.2
ENSG00000273269	ENST00000422269.1	n.*410-55G>A		intron_variant	Intron 6 of 8	2		ENSP00000476793.1
STPG4	ENST00000449846.5	c.156+8733G>A		intron_variant	Intron 3 of 4	3		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

Gnomad4 AFR exome AF: 0.429

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.872

Gnomad4 NFE exome AF: 0.767

Gnomad4 OTH exome AF: 0.724

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

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.726

Alfa AF: 0.755 Hom.: 50421

Bravo AF: 0.667

Asia WGS AF: 0.877 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.71

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: rs1880583; hg19: chr2-47348347;