ENST00000522676.5:c.463-132493C>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522676.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STPG2	ENST00000522676.5	TSL:1	c.463-132493C>A		intron	N/A	ENSP00000428346.1
	STPG2	ENST00000506482.1	TSL:4	n.269-56745C>A		intron	N/A

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

African (AFR) AF: 0.210 AC: 8691 AN: 41428

American (AMR) AF: 0.164 AC: 2496 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5162

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4816

European-Finnish (FIN) AF: 0.0955 AC: 1008 AN: 10550

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4892 AN: 67960

Other (OTH) AF: 0.122 AC: 259 AN: 2116

Alfa AF: 0.0812 Hom.: 272

Bravo AF: 0.133

Asia WGS AF: 0.0860 AC: 299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.34
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs28539905; hg19: chr4-98241477;