dbSNP rs3194168: SGF29:p.Glu289Glu (chr16-28591691-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_138414.3(SGF29):c.867A>G(p.Glu289Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,607,920 control chromosomes in the GnomAD database, including 11,371 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 0.11 ( 959 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10412 hom. )

Consequence

SGF29
NM_138414.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52

Publications

14 publications found

Variant links:

Genes affected

SGF29 (HGNC:25156): (SAGA complex associated factor 29) CCDC101 is a subunit of 2 histone acetyltransferase complexes: the ADA2A (TADA2A; MIM 602276)-containing (ATAC) complex and the SPT3 (SUPT3H; MIM 602947)-TAF9 (MIM 600822)-GCN5 (KAT2A; MIM 602301)/PCAF (KAT2B; MIM 602303) acetylase (STAGA) complex. Both of these complexes contain either GCN5 or PCAF, which are paralogous acetyltransferases (Wang et al., 2008 [PubMed 18838386]).[supplied by OMIM, Apr 2010]

SGF29 links:

ENSG00000289754 (HGNC:):

ENSG00000289754 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=1.52 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGF29	NM_138414.3 link	c.867A>G	p.Glu289Glu	synonymous_variant	Exon 10 of 10	ENST00000317058.8	NP_612423.1	Q96ES7
SGF29	XM_017022894.2 link	c.*639A>G		3_prime_UTR_variant	Exon 10 of 10		XP_016878383.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGF29	ENST00000317058.8 link	c.867A>G	p.Glu289Glu	synonymous_variant	Exon 10 of 10	1	NM_138414.3	ENSP00000316114.3		Q96ES7

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16252

AN:

151968

Hom.:

958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0830

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.00232

Gnomad SAS

AF:

0.0948

Gnomad FIN

AF:

0.0909

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.133

GnomAD2 exomes

AF:

0.0996

AC:

25003

AN:

250972

AF XY:

0.102

show subpopulations

Gnomad AFR exome

AF:

0.0829

Gnomad AMR exome

AF:

0.0674

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.000816

Gnomad FIN exome

AF:

0.0889

Gnomad NFE exome

AF:

0.124

Gnomad OTH exome

AF:

0.117

GnomAD4 exome

AF:

0.115

AC:

167342

AN:

1455834

Hom.:

10412

Cov.:

AF XY:

0.115

AC XY:

83297

AN XY:

724508

show subpopulations

African (AFR)

AF:

0.0847

AC:

2825

AN:

33364

American (AMR)

AF:

0.0699

AC:

3123

AN:

44680

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

4293

AN:

26068

East Asian (EAS)

AF:

0.000529

AC:

AN:

39690

South Asian (SAS)

AF:

0.0951

AC:

8194

AN:

86138

European-Finnish (FIN)

AF:

0.0873

AC:

4663

AN:

53384

Middle Eastern (MID)

AF:

0.181

AC:

1041

AN:

5760

European-Non Finnish (NFE)

AF:

0.123

AC:

136066

AN:

1106548

Other (OTH)

AF:

0.118

AC:

7116

AN:

60202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.423

Heterozygous variant carriers

6761

13522

20284

27045

33806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4828

9656

14484

19312

24140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.107

AC:

16256

AN:

152086

Hom.:

959

Cov.:

AF XY:

0.105

AC XY:

7815

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.0829

AC:

3441

AN:

41492

American (AMR)

AF:

0.113

AC:

1720

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

578

AN:

3470

East Asian (EAS)

AF:

0.00233

AC:

AN:

5158

South Asian (SAS)

AF:

0.0951

AC:

458

AN:

4818

European-Finnish (FIN)

AF:

0.0909

AC:

964

AN:

10602

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8514

AN:

67948

Other (OTH)

AF:

0.132

AC:

279

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

753

1506

2258

3011

3764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.117

Hom.:

497

Bravo

AF:

0.108

Asia WGS

AF:

0.0480

AC:

166

AN:

3478

EpiCase

AF:

0.137

EpiControl

AF:

0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.1

(source)

DANN

Benign

0.61

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over