6-45213957-T-A

Position:

• chr6-45213957-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003599.4(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 NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.102-107951A>T		intron_variant		ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.102-107951A>T		intron_variant		1	NM_003599.4	ENSP00000360514	P1
SUPT3H	ENST00000371460.5	c.134+107839A>T		intron_variant		1		ENSP00000360515
SUPT3H	ENST00000475057.5	c.102-107951A>T		intron_variant, NMD_transcript_variant		2		ENSP00000436411

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

Gnomad4 AFR AF: 0.0101

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.0250

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0724

Gnomad4 NFE AF: 0.0544

Gnomad4 OTH AF: 0.0308

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.61

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: rs10456544; hg19: chr6-45181694;