rs783919

chr4-98027799-A-G

Variant summary

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

The NM_174952.3(STPG2):c.613-46481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,192 control chromosomes in the GnomAD database, including 56,282 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 0.86 (56282 hom., cov: 32)
• Consequence: STPG2 NM_174952.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

STPG2 (HGNC:28712): (sperm tail PG-rich repeat containing 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STPG2	NM_174952.3	c.613-46481T>C		intron_variant		ENST00000295268.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STPG2	ENST00000295268.4	c.613-46481T>C		intron_variant		1	NM_174952.3	P1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130601 AN: 152074 Hom.: 56232 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.859 AC: 130708 AN: 152192 Hom.: 56282 Cov.: 32 AF XY: 0.856 AC XY: 63703 AN XY: 74392

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.886

Alfa AF: 0.878 Hom.: 75764

Bravo AF: 0.864

Asia WGS AF: 0.825 AC: 2867 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	2.2
Dann	Benign	0.44

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: rs783919; hg19: chr4-98948950;