rs7691268

chr4-97312809-A-G

Variant summary

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

The ENST00000522676.5(STPG2):c.463-124976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,130 control chromosomes in the GnomAD database, including 438 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 0.066 (438 hom., cov: 32)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 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.463-124976T>C		intron_variant		1
STPG2	ENST00000506482.1	n.269-49228T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10000 AN: 152012 Hom.: 435 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0658 AC: 10015 AN: 152130 Hom.: 438 Cov.: 32 AF XY: 0.0683 AC XY: 5080 AN XY: 74366

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.0588

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0667 Hom.: 190

Bravo AF: 0.0690

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.0
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7691268; hg19: chr4-98233960;