NM_003599.4:c.102-21420T>G

Variant names:

• chr6-45127426-A-C
• rs9395066
• NM_003599.4:c.102-21420T>G

Variant summary

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

The NM_003599.4(SUPT3H):​c.102-21420T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,940 control chromosomes in the GnomAD database, including 12,636 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 0.40 (12636 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 26 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.102-21420T>G		intron_variant	Intron 2 of 10	ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.102-21420T>G		intron_variant	Intron 2 of 10	1	NM_003599.4	ENSP00000360514.1
SUPT3H	ENST00000371460.5	c.135-21420T>G		intron_variant	Intron 4 of 12	1		ENSP00000360515.1
SUPT3H	ENST00000475057.5	n.102-21420T>G		intron_variant	Intron 2 of 11	2		ENSP00000436411.1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60984 AN: 151822 Hom.: 12623 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.402 AC: 61023 AN: 151940 Hom.: 12636 Cov.: 32 AF XY: 0.403 AC XY: 29889 AN XY: 74248

African (AFR) AF: 0.344 AC: 14224 AN: 41408

American (AMR) AF: 0.376 AC: 5740 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1601 AN: 3466

East Asian (EAS) AF: 0.709 AC: 3664 AN: 5170

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4816

European-Finnish (FIN) AF: 0.406 AC: 4288 AN: 10550

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27590 AN: 67938

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.405 Hom.: 41111

Bravo AF: 0.397

Asia WGS AF: 0.580 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.81
PhyloP100		-0.14
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: rs9395066; hg19: chr6-45095163;