chr16-28571894-G-A

Variant names:

• chr16-28571894-G-A
• rs151230
• NM_138414.3:c.-15-9161G>A

Variant summary

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

The NM_138414.3(SGF29):​c.-15-9161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,274 control chromosomes in the GnomAD database, including 1,026 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 (1026 hom., cov: 32)
• Consequence: SGF29 NM_138414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 17 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=-0.94).
• 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.-15-9161G>A		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.-15-9161G>A		intron	N/A	ENSP00000316114.3
	SGF29	ENST00000564682.5	TSL:2	n.184-9161G>A		intron	N/A
	SGF29	ENST00000567564.1	TSL:5	n.-15-9161G>A		intron	N/A	ENSP00000455370.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16950 AN: 152156 Hom.: 1025 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.111 AC: 16953 AN: 152274 Hom.: 1026 Cov.: 32 AF XY: 0.109 AC XY: 8133 AN XY: 74450

African (AFR) AF: 0.0983 AC: 4084 AN: 41548

American (AMR) AF: 0.115 AC: 1759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5188

South Asian (SAS) AF: 0.0947 AC: 457 AN: 4826

European-Finnish (FIN) AF: 0.0908 AC: 963 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8524 AN: 68030

Other (OTH) AF: 0.134 AC: 284 AN: 2116

Alfa AF: 0.122 Hom.: 2032

Bravo AF: 0.113

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.83
PhyloP100		-2.7
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: rs151230; hg19: chr16-28583215;