rs10516422

chr4-97343809-A-G

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)

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STPG2	ENST00000522676.5	c.463-155976T>C		intron_variant		1
	ENST00000521680.5	n.422-9096T>C		intron_variant, non_coding_transcript_variant		3
STPG2	ENST00000506482.1	n.269-80228T>C		intron_variant, non_coding_transcript_variant		4

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;