Variant chr16-28591691-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_138414.3(SGF29):c.867A>G(p.Glu289=) 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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SGF29	NM_138414.3 linkuse as main transcript	c.867A>G	p.Glu289=	synonymous_variant	10/10	ENST00000317058.8
SGF29	XM_017022894.2 linkuse as main transcript	c.*639A>G		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
SGF29	ENST00000317058.8 linkuse as main transcript	c.867A>G	p.Glu289=	synonymous_variant	10/10	1	NM_138414.3	P1
SGF29	ENST00000564023.1 linkuse as main transcript	c.258A>G	p.Glu86=	synonymous_variant	4/4	5
SGF29	ENST00000565945.1 linkuse as main transcript	n.438A>G		non_coding_transcript_exon_variant	2/2	2
SGF29	ENST00000567447.1 linkuse as main transcript	n.627A>G		non_coding_transcript_exon_variant	4/4	2

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

GnomAD3 exomes

AF:

0.0996

AC:

25003

AN:

250972

Hom.:

1452

AF XY:

0.102

AC XY:

13887

AN XY:

135618

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 SAS exome

AF:

0.0955

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

Gnomad4 AFR exome

AF:

0.0847

Gnomad4 AMR exome

AF:

0.0699

Gnomad4 ASJ exome

AF:

0.165

Gnomad4 EAS exome

AF:

0.000529

Gnomad4 SAS exome

AF:

0.0951

Gnomad4 FIN exome

AF:

0.0873

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.107

AC:

16256

AN:

152086

Hom.:

959

Cov.:

AF XY:

0.105

AC XY:

7815

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.0829

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.167

Gnomad4 EAS

AF:

0.00233

Gnomad4 SAS

AF:

0.0951

Gnomad4 FIN

AF:

0.0909

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.117

Hom.:

496

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

DANN

Benign

0.61

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