6-45132817-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUPT3H	NM_003599.4	c.102-26811G>A		intron_variant		ENST00000371459.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUPT3H	ENST00000371459.6	c.102-26811G>A		intron_variant		1	NM_003599.4	P1
SUPT3H	ENST00000371460.5	c.135-26811G>A		intron_variant		1
SUPT3H	ENST00000475057.5	c.102-26811G>A		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.861

Alfa AF: 0.866 Hom.: 6678

Bravo AF: 0.861

Asia WGS AF: 0.814 AC: 2827 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs1285006; hg19: chr6-45100554;