16-28583228-A-G

Variant names:

• chr16-28583228-A-G
• rs4788073
• NM_138414.3:c.76-1685A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138414.3(SGF29):​c.76-1685A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,136 control chromosomes in the GnomAD database, including 8,717 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 0.32 (8717 hom., cov: 33)
• Consequence: SGF29 NM_138414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 30 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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.76-1685A>G		intron	N/A	NP_612423.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGF29	ENST00000317058.8	TSL:1 MANE Select	c.76-1685A>G		intron	N/A	ENSP00000316114.3
	SGF29	ENST00000564682.5	TSL:2	n.274-1685A>G		intron	N/A
	SGF29	ENST00000567564.1	TSL:5	n.76-1685A>G		intron	N/A	ENSP00000455370.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48899 AN: 152018 Hom.: 8706 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.322 AC: 48948 AN: 152136 Hom.: 8717 Cov.: 33 AF XY: 0.321 AC XY: 23857 AN XY: 74356

African (AFR) AF: 0.238 AC: 9891 AN: 41514

American (AMR) AF: 0.339 AC: 5176 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3466

East Asian (EAS) AF: 0.0771 AC: 400 AN: 5186

South Asian (SAS) AF: 0.197 AC: 949 AN: 4826

European-Finnish (FIN) AF: 0.469 AC: 4953 AN: 10568

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25779 AN: 67988

Other (OTH) AF: 0.294 AC: 620 AN: 2110

Alfa AF: 0.353 Hom.: 42013

Bravo AF: 0.311

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.77
PhyloP100		0.11
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: rs4788073; hg19: chr16-28594549;