4-97349649-T-C

Variant summary

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

The ENST00000522676.5(STPG2):c.463-161816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,834 control chromosomes in the GnomAD database, including 18,236 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 0.47 (18236 hom., cov: 31)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

Genes affected

STPG2 (HGNC:28712): (sperm tail PG-rich repeat containing 2)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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.463-161816A>G		intron_variant		1
	ENST00000521680.5	n.422-14936A>G		intron_variant, non_coding_transcript_variant		3
STPG2	ENST00000506482.1	n.269-86068A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71899 AN: 151714 Hom.: 18201 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.474 AC: 71992 AN: 151834 Hom.: 18236 Cov.: 31 AF XY: 0.473 AC XY: 35092 AN XY: 74198

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.471

Alfa AF: 0.399 Hom.: 24715

Bravo AF: 0.497

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.86
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1462767; hg19: chr4-98270800;