chr4-97306224-G-T

Variant names:

• chr4-97306224-G-T
• rs13119820
• ENST00000522676.5:c.463-118391C>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STPG2	ENST00000522676.5	c.463-118391C>A		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1	n.269-42643C>A		intron_variant	Intron 2 of 4	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;