rs13119820

Positions:

• chr4-97306224-G-T

Variant summary

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

The ENST00000522676.5(STPG2):​c.463-118391C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,650 control chromosomes in the GnomAD database, including 14,222 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 0.43 (14222 hom., cov: 32)
• Consequence: STPG2 ENST00000522676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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.463-118391C>A		intron_variant		1
STPG2	ENST00000506482.1	n.269-42643C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64671 AN: 151532 Hom.: 14190 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.427 AC: 64756 AN: 151650 Hom.: 14222 Cov.: 32 AF XY: 0.427 AC XY: 31666 AN XY: 74094

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.432

Alfa AF: 0.392 Hom.: 24106

Bravo AF: 0.445

Asia WGS AF: 0.502 AC: 1744 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13119820; hg19: chr4-98227375;