rs7691268

Variant names:

• chr4-97312809-A-G
• rs7691268
• ENST00000522676.5:c.463-124976T>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000522676.5	c.463-124976T>C		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.269-49228T>C		intron_variant	Intron 2 of 4	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;