Variant rs2229358 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003110.6(SP2):c.717G>A(p.Pro239Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,613,216 control chromosomes in the GnomAD database, including 162,322 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 ( 14462 hom., cov: 32)

Exomes 𝑓: 0.44 ( 147860 hom. )

Consequence

SP2
NM_003110.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.86

Variant links:

Genes affected

SP2 (HGNC:11207): (Sp2 transcription factor) This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. [provided by RefSeq, Jul 2008]

SP2 links:

SP2-AS1 (HGNC:):

SP2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-3.86 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SP2	NM_003110.6 linkuse as main transcript	c.717G>A	p.Pro239Pro	synonymous_variant	3/7	ENST00000376741.5	NP_003101.3	Q02086-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SP2	ENST00000376741.5 linkuse as main transcript	c.717G>A	p.Pro239Pro	synonymous_variant	3/7	1	NM_003110.6	ENSP00000365931.4		Q02086-1

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65335

AN:

151950

Hom.:

14449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.470

GnomAD3 exomes

AF:

0.463

AC:

116318

AN:

251054

Hom.:

28196

AF XY:

0.466

AC XY:

63202

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.423

Gnomad ASJ exome

AF:

0.502

Gnomad EAS exome

AF:

0.760

Gnomad SAS exome

AF:

0.489

Gnomad FIN exome

AF:

0.449

Gnomad NFE exome

AF:

0.435

Gnomad OTH exome

AF:

0.477

GnomAD4 exome

AF:

0.445

AC:

649742

AN:

1461148

Hom.:

147860

Cov.:

AF XY:

0.446

AC XY:

324451

AN XY:

726882

show subpopulations

Gnomad4 AFR exome

AF:

0.351

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.501

Gnomad4 EAS exome

AF:

0.768

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.450

Gnomad4 NFE exome

AF:

0.430

Gnomad4 OTH exome

AF:

0.457

GnomAD4 genome

AF:

0.430

AC:

65386

AN:

152068

Hom.:

14462

Cov.:

AF XY:

0.431

AC XY:

32017

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.358

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.496

Gnomad4 EAS

AF:

0.759

Gnomad4 SAS

AF:

0.476

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.477

Alfa

AF:

0.443

Hom.:

35723

Bravo

AF:

0.425

Asia WGS

AF:

0.593

AC:

2061

AN:

3478

EpiCase

AF:

0.449

EpiControl

AF:

0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.076

DANN

Benign

0.74

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over