4-97320326-G-T

Variant names:

• chr4-97320326-G-T
• rs28539905
• ENST00000522676.5:c.463-132493C>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000522676.5	c.463-132493C>A		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.269-56745C>A		intron_variant	Intron 2 of 4	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;