4-97320326-G-T

Variant summary

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

The ENST00000522676.5(STPG2):c.463-132493C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,960 control chromosomes in the GnomAD database, including 1,381 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 0.12 (1381 hom., cov: 32)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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.463-132493C>A		intron_variant		1
STPG2	ENST00000506482.1	n.269-56745C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18394 AN: 151842 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.0955

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.121 AC: 18418 AN: 151960 Hom.: 1381 Cov.: 32 AF XY: 0.122 AC XY: 9055 AN XY: 74284

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0955

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0663 Hom.: 127

Bravo AF: 0.133

Asia WGS AF: 0.0860 AC: 299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.72
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28539905; hg19: chr4-98241477;