rs10948172

Variant names:

• chr6-44809954-A-G
• rs10948172
• ENST00000475057.5:n.*53-453T>C

Variant summary

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

The ENST00000475057.5(SUPT3H):​n.*53-453T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,070 control chromosomes in the GnomAD database, including 5,808 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 0.27 (5808 hom., cov: 32)
• Consequence: SUPT3H ENST00000475057.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 46 publications found

Genes affected

SUPT3H (HGNC:11466): (SPT3 homolog, SAGA and STAGA complex component) Enables transcription coactivator activity. Involved in histone H3 acetylation and histone deubiquitination. Located in nucleoplasm. Part of SAGA complex and transcription factor TFTC complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286417 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000475057.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT3H	NR_146632.2		n.1174-453T>C		intron	N/A
	SUPT3H	NR_146633.1		n.1166-453T>C		intron	N/A
	SUPT3H	NR_146634.2		n.1160-453T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT3H	ENST00000475057.5	TSL:2	n.*53-453T>C		intron	N/A	ENSP00000436411.1	O75486-1
	ENSG00000286417	ENST00000671451.2		n.196-19634A>G		intron	N/A
	ENSG00000286417	ENST00000811306.1		n.275-19634A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40908 AN: 151952 Hom.: 5798 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.269 AC: 40938 AN: 152070 Hom.: 5808 Cov.: 32 AF XY: 0.266 AC XY: 19794 AN XY: 74314

African (AFR) AF: 0.300 AC: 12434 AN: 41476

American (AMR) AF: 0.205 AC: 3140 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3468

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5180

South Asian (SAS) AF: 0.173 AC: 836 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3107 AN: 10566

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19627 AN: 67958

Other (OTH) AF: 0.251 AC: 529 AN: 2110

Alfa AF: 0.276 Hom.: 26541

Bravo AF: 0.264

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10948172; hg19: chr6-44777691;