Genetic Variant STPG2:c.463-132493C>A (chr4-97320326-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000522676.5(STPG2):c.463-132493C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,960 control chromosomes in the GnomAD database, including 1,381 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 0.12 ( 1381 hom., cov: 32)

Consequence

STPG2
ENST00000522676.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130

Publications

1 publications found

Variant links:

Genes affected

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

STPG2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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 link	c.463-132493C>A		intron_variant	Intron 4 of 4	1		ENSP00000428346.1		H0YAZ7
STPG2	ENST00000506482.1 link	n.269-56745C>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18394

AN:

151842

Hom.:

1381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.0879

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.0591

Gnomad FIN

AF:

0.0955

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0720

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.121

AC:

18418

AN:

151960

Hom.:

1381

Cov.:

AF XY:

0.122

AC XY:

9055

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.210

AC:

8691

AN:

41428

American (AMR)

AF:

0.164

AC:

2496

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.0455

AC:

158

AN:

3470

East Asian (EAS)

AF:

0.101

AC:

521

AN:

5162

South Asian (SAS)

AF:

0.0590

AC:

284

AN:

4816

European-Finnish (FIN)

AF:

0.0955

AC:

1008

AN:

10550

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0720

AC:

4892

AN:

67960

Other (OTH)

AF:

0.122

AC:

259

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

787

1574

2360

3147

3934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0812

Hom.:

272

Bravo

AF:

0.133

Asia WGS

AF:

0.0860

AC:

299

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.72

(source)

DANN

Benign

0.34

PhyloP100

-0.013

Splicing

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

Publications

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4-97320326-G-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over