16-28571894-G-A

Position:

• chr16-28571894-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGF29	NM_138414.3	c.-15-9161G>A		intron_variant		ENST00000317058.8	NP_612423.1
SGF29	XM_017022894.2	c.-15-9161G>A		intron_variant			XP_016878383.1
SGF29	XR_001751821.2	n.179-9161G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGF29	ENST00000317058.8	c.-15-9161G>A		intron_variant		1	NM_138414.3	ENSP00000316114	P1
SGF29	ENST00000567564.1	c.-15-9161G>A		intron_variant, NMD_transcript_variant		5		ENSP00000455370
SGF29	ENST00000564682.5	n.184-9161G>A		intron_variant, non_coding_transcript_variant		2
SGF29	ENST00000569581.1	n.179-9161G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.0908

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.134

Alfa AF: 0.124 Hom.: 1615

Bravo AF: 0.113

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.83

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

Other links and lift over

dbSNP: rs151230; hg19: chr16-28583215;