rs10521145

Positions:

• chr16-28585563-G-A
• chr16-28585563-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138414.3(SGF29):​c.152-85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,227,602 control chromosomes in the GnomAD database, including 8,543 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 (960 hom., cov: 32)
  • Exomes 𝑓: 0.11 (7583 hom.)
• Consequence: SGF29 NM_138414.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

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=-0.95).
• 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.152-85G>A		intron_variant		ENST00000317058.8	NP_612423.1
SGF29	XM_017022894.2	c.152-85G>A		intron_variant			XP_016878383.1
SGF29	XR_001751821.2	n.345-85G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGF29	ENST00000317058.8	c.152-85G>A		intron_variant		1	NM_138414.3	ENSP00000316114	P1
SGF29	ENST00000567564.1	c.152-85G>A		intron_variant, NMD_transcript_variant		5		ENSP00000455370
SGF29	ENST00000569581.1	n.345-85G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16212 AN: 152138 Hom.: 960 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.114 AC: 122585 AN: 1075346 Hom.: 7583 Cov.: 15 AF XY: 0.114 AC XY: 62903 AN XY: 551516

Gnomad4 AFR exome AF: 0.0864

Gnomad4 AMR exome AF: 0.0700

Gnomad4 ASJ exome AF: 0.164

Gnomad4 EAS exome AF: 0.000877

Gnomad4 SAS exome AF: 0.0962

Gnomad4 FIN exome AF: 0.0873

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.106 AC: 16215 AN: 152256 Hom.: 960 Cov.: 32 AF XY: 0.105 AC XY: 7794 AN XY: 74438

Gnomad4 AFR AF: 0.0824

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.130

Alfa AF: 0.122 Hom.: 1364

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.094
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10521145; hg19: chr16-28596884;