rs969049

chr4-98067706-C-T

Variant summary

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

The NM_174952.3(STPG2):c.612+38247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,914 control chromosomes in the GnomAD database, including 12,374 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 0.40 (12374 hom., cov: 32)
• Consequence: STPG2 NM_174952.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STPG2	NM_174952.3	c.612+38247G>A		intron_variant		ENST00000295268.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STPG2	ENST00000295268.4	c.612+38247G>A		intron_variant		1	NM_174952.3	P1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60639 AN: 151798 Hom.: 12369 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.399 AC: 60665 AN: 151914 Hom.: 12374 Cov.: 32 AF XY: 0.393 AC XY: 29195 AN XY: 74266

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.393

Alfa AF: 0.392 Hom.: 1482

Bravo AF: 0.402

Asia WGS AF: 0.387 AC: 1341 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs969049; hg19: chr4-98988857;