rs783919

Variant names:

• chr4-98027799-A-G
• rs783919
• NM_174952.3:c.613-46481T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STPG2	NM_174952.3	c.613-46481T>C		intron_variant	Intron 5 of 10	ENST00000295268.4	NP_777612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000295268.4	c.613-46481T>C		intron_variant	Intron 5 of 10	1	NM_174952.3	ENSP00000295268.3

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

African (AFR) AF: 0.854 AC: 35473 AN: 41534

American (AMR) AF: 0.883 AC: 13490 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3019 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3494 AN: 5168

South Asian (SAS) AF: 0.905 AC: 4365 AN: 4822

European-Finnish (FIN) AF: 0.794 AC: 8409 AN: 10590

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59476 AN: 68000

Other (OTH) AF: 0.886 AC: 1874 AN: 2116

Alfa AF: 0.877 Hom.: 96572

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
PhyloP100		-0.79
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: rs783919; hg19: chr4-98948950;