rs10456544

Variant names:

• chr6-45213957-T-A
• rs10456544
• NM_003599.4:c.102-107951A>T

Variant summary

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

The ENST00000371459.6(SUPT3H):​c.102-107951A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 134,658 control chromosomes in the GnomAD database, including 120 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 0.037 (120 hom., cov: 30)
• Consequence: SUPT3H ENST00000371459.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371459.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT3H	NM_003599.4	MANE Select	c.102-107951A>T		intron	N/A	NP_003590.1
	SUPT3H	NM_181356.3		c.134+107839A>T		intron	N/A	NP_852001.1
	SUPT3H	NM_001350324.2		c.102-107951A>T		intron	N/A	NP_001337253.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT3H	ENST00000371459.6	TSL:1 MANE Select	c.102-107951A>T		intron	N/A	ENSP00000360514.1
	SUPT3H	ENST00000371460.5	TSL:1	c.134+107839A>T		intron	N/A	ENSP00000360515.1
	SUPT3H	ENST00000475057.5	TSL:2	n.102-107951A>T		intron	N/A	ENSP00000436411.1

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 4935 AN: 134600 Hom.: 120 Cov.: 30

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0391

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0250

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.0172

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0366 AC: 4935 AN: 134658 Hom.: 120 Cov.: 30 AF XY: 0.0364 AC XY: 2330 AN XY: 63934

African (AFR) AF: 0.0101 AC: 359 AN: 35420

American (AMR) AF: 0.0233 AC: 278 AN: 11956

Ashkenazi Jewish (ASJ) AF: 0.0250 AC: 85 AN: 3406

East Asian (EAS) AF: 0.00 AC: 0 AN: 4428

South Asian (SAS) AF: 0.0158 AC: 66 AN: 4176

European-Finnish (FIN) AF: 0.0724 AC: 484 AN: 6686

Middle Eastern (MID) AF: 0.0183 AC: 4 AN: 218

European-Non Finnish (NFE) AF: 0.0544 AC: 3567 AN: 65624

Other (OTH) AF: 0.0308 AC: 57 AN: 1850

Alfa AF: 0.0413 Hom.: 19

Bravo AF: 0.0305

Asia WGS AF: 0.00724 AC: 25 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.61
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism

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: rs10456544; hg19: chr6-45181694;