16-28578398-A-G

Variant names:

• chr16-28578398-A-G
• rs11641853
• NM_138414.3:c.-15-2657A>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.-15-2657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,088 control chromosomes in the GnomAD database, including 917 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 0.10 (917 hom., cov: 31)
• Consequence: SGF29 NM_138414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 11 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=-1.03).
• 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.-15-2657A>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.-15-2657A>G		intron	N/A	ENSP00000316114.3
	SGF29	ENST00000564682.5	TSL:2	n.184-2657A>G		intron	N/A
	SGF29	ENST00000567564.1	TSL:5	n.-15-2657A>G		intron	N/A	ENSP00000455370.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15581 AN: 151970 Hom.: 917 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.102 AC: 15581 AN: 152088 Hom.: 917 Cov.: 31 AF XY: 0.101 AC XY: 7481 AN XY: 74346

African (AFR) AF: 0.0681 AC: 2827 AN: 41498

American (AMR) AF: 0.110 AC: 1677 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5176

South Asian (SAS) AF: 0.0946 AC: 456 AN: 4822

European-Finnish (FIN) AF: 0.0908 AC: 958 AN: 10554

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8513 AN: 67996

Other (OTH) AF: 0.129 AC: 271 AN: 2108

Alfa AF: 0.121 Hom.: 1475

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.18
PhyloP100		-0.59
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: rs11641853; hg19: chr16-28589719; COSMIC: COSV57683222;