rs10521145

Variant names:

• chr16-28585563-G-A
• rs10521145
• NM_138414.3:c.152-85G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 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=-0.95).
• 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 rank	MANE	Protein	UniProt
SGF29	NM_138414.3	c.152-85G>A		intron_variant	Intron 3 of 9	ENST00000317058.8	NP_612423.1
SGF29	XM_017022894.2	c.152-85G>A		intron_variant	Intron 3 of 9		XP_016878383.1
SGF29	XR_001751821.2	n.345-85G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGF29	ENST00000317058.8	c.152-85G>A		intron_variant	Intron 3 of 9	1	NM_138414.3	ENSP00000316114.3

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

African (AFR) AF: 0.0864 AC: 2219 AN: 25686

American (AMR) AF: 0.0700 AC: 3041 AN: 43468

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 3867 AN: 23564

East Asian (EAS) AF: 0.000877 AC: 33 AN: 37634

South Asian (SAS) AF: 0.0962 AC: 7490 AN: 77876

European-Finnish (FIN) AF: 0.0873 AC: 4593 AN: 52592

Middle Eastern (MID) AF: 0.182 AC: 923 AN: 5078

European-Non Finnish (NFE) AF: 0.124 AC: 94768 AN: 761784

Other (OTH) AF: 0.119 AC: 5651 AN: 47664

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

African (AFR) AF: 0.0824 AC: 3422 AN: 41550

American (AMR) AF: 0.112 AC: 1716 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5174

South Asian (SAS) AF: 0.0948 AC: 458 AN: 4830

European-Finnish (FIN) AF: 0.0906 AC: 962 AN: 10616

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

European-Non Finnish (NFE) AF: 0.125 AC: 8509 AN: 68012

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.120 Hom.: 1903

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
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10521145; hg19: chr16-28596884;