rs10516422

Variant names:

• chr4-97343809-A-G
• rs10516422
• ENST00000522676.5:c.463-155976T>C

Variant summary

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

The ENST00000522676.5(STPG2):​c.463-155976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,264 control chromosomes in the GnomAD database, including 924 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 0.10 (924 hom., cov: 33)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

Genes affected

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

ENSG00000254044 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000522676.5	c.463-155976T>C		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.269-80228T>C		intron_variant	Intron 2 of 4	4
ENSG00000254044	ENST00000521680.5	n.422-9096T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15725 AN: 152148 Hom.: 922 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.103 AC: 15747 AN: 152264 Hom.: 924 Cov.: 33 AF XY: 0.105 AC XY: 7781 AN XY: 74454

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0716

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0798 Hom.: 763

Bravo AF: 0.112

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10516422; hg19: chr4-98264960;