dbSNP rs13119820: STPG2:c.463-118391C>A (chr4-97306224-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.463-118391C>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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.399

Publications

1 publications found

Variant links:

Genes affected

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

STPG2 links:

Genome browser will be placed here

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=-0.92).

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 link	c.463-118391C>A		intron_variant	Intron 4 of 4	1		ENSP00000428346.1
STPG2	ENST00000506482.1 link	n.269-42643C>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64671

AN:

151532

Hom.:

14190

Cov.:

show subpopulations

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.:

AF XY:

0.427

AC XY:

31666

AN XY:

74094

show subpopulations

African (AFR)

AF:

0.513

AC:

21246

AN:

41380

American (AMR)

AF:

0.477

AC:

7239

AN:

15176

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

1127

AN:

3466

East Asian (EAS)

AF:

0.455

AC:

2321

AN:

5104

South Asian (SAS)

AF:

0.507

AC:

2447

AN:

4826

European-Finnish (FIN)

AF:

0.288

AC:

3036

AN:

10540

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25847

AN:

67848

Other (OTH)

AF:

0.432

AC:

910

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1890

3781

5671

7562

9452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.401

Hom.:

38984

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

(source)

DANN

Benign

0.42

PhyloP100

-0.40

Splicing

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

Publications

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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