chr16-28591691-A-G

Variant names:

• chr16-28591691-A-G
• rs3194168
• NM_138414.3:c.867A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 14 publications found

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]

ENSG00000289754 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138414.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGF29	NM_138414.3	MANE Select	c.867A>G	p.Glu289Glu	synonymous	Exon 10 of 10	NP_612423.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGF29	ENST00000317058.8	TSL:1 MANE Select	c.867A>G	p.Glu289Glu	synonymous	Exon 10 of 10	ENSP00000316114.3
	SGF29	ENST00000564023.1	TSL:5	c.255A>G	p.Glu85Glu	synonymous	Exon 4 of 4	ENSP00000454730.1
	SGF29	ENST00000565945.1	TSL:2	n.438A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16252 AN: 151968 Hom.: 958 Cov.: 32

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

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.: 31 AF XY: 0.115 AC XY: 83297 AN XY: 724508

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: 21 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

GnomAD4 genome AF: 0.107 AC: 16256 AN: 152086 Hom.: 959 Cov.: 32 AF XY: 0.105 AC XY: 7815 AN XY: 74338

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: 12 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: 54 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8514 AN: 67948

Other (OTH) AF: 0.132 AC: 279 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.1
DANN	Benign	0.61
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3194168; hg19: chr16-28603012; COSMIC: COSV57680879; COSMIC: COSV57680879;