NM_003599.4:c.102-26811G>A

Variant names:

• chr6-45132817-C-T
• rs1285006
• NM_003599.4:c.102-26811G>A

Variant summary

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

The NM_003599.4(SUPT3H):​c.102-26811G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,168 control chromosomes in the GnomAD database, including 57,769 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 0.87 (57769 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003599.4. 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	NM_003599.4	MANE Select	c.102-26811G>A		intron	N/A	NP_003590.1	O75486-1
	SUPT3H	NM_181356.3		c.135-26811G>A		intron	N/A	NP_852001.1	O75486-4
	SUPT3H	NM_001350324.2		c.102-26811G>A		intron	N/A	NP_001337253.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT3H	ENST00000371459.6	TSL:1 MANE Select	c.102-26811G>A		intron	N/A	ENSP00000360514.1	O75486-1
	SUPT3H	ENST00000371460.5	TSL:1	c.135-26811G>A		intron	N/A	ENSP00000360515.1	O75486-4
	SUPT3H	ENST00000889037.1		c.156-26811G>A		intron	N/A	ENSP00000559096.1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132217 AN: 152050 Hom.: 57724 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.870 AC: 132316 AN: 152168 Hom.: 57769 Cov.: 32 AF XY: 0.866 AC XY: 64406 AN XY: 74392

African (AFR) AF: 0.911 AC: 37856 AN: 41544

American (AMR) AF: 0.769 AC: 11742 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2886 AN: 3466

East Asian (EAS) AF: 0.740 AC: 3825 AN: 5170

South Asian (SAS) AF: 0.866 AC: 4173 AN: 4820

European-Finnish (FIN) AF: 0.874 AC: 9252 AN: 10588

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.877 AC: 59666 AN: 67996

Other (OTH) AF: 0.861 AC: 1821 AN: 2114

Alfa AF: 0.867 Hom.: 6996

Bravo AF: 0.861

Asia WGS AF: 0.814 AC: 2827 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.55
PhyloP100		-1.3
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: rs1285006; hg19: chr6-45100554;