NM_003599.4:c.505-16941A>T

Variant names:

• chr6-44978769-T-A
• rs9472414
• NM_003599.4:c.505-16941A>T

Variant summary

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

The NM_003599.4(SUPT3H):​c.505-16941A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,784 control chromosomes in the GnomAD database, including 4,563 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 0.24 (4563 hom., cov: 31)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 35 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.505-16941A>T		intron_variant	Intron 6 of 10	ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.505-16941A>T		intron_variant	Intron 6 of 10	1	NM_003599.4	ENSP00000360514.1
SUPT3H	ENST00000371460.5	c.538-16941A>T		intron_variant	Intron 8 of 12	1		ENSP00000360515.1
SUPT3H	ENST00000637763.2	c.319-16941A>T		intron_variant	Intron 4 of 8	3		ENSP00000490652.2
SUPT3H	ENST00000475057.5	n.505-16941A>T		intron_variant	Intron 6 of 11	2		ENSP00000436411.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36236 AN: 151666 Hom.: 4558 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.239 AC: 36269 AN: 151784 Hom.: 4563 Cov.: 31 AF XY: 0.243 AC XY: 18019 AN XY: 74178

African (AFR) AF: 0.234 AC: 9695 AN: 41376

American (AMR) AF: 0.371 AC: 5658 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1410 AN: 5144

South Asian (SAS) AF: 0.210 AC: 1005 AN: 4796

European-Finnish (FIN) AF: 0.232 AC: 2444 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14377 AN: 67894

Other (OTH) AF: 0.251 AC: 529 AN: 2104

Alfa AF: 0.225 Hom.: 2142

Bravo AF: 0.252

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.63
DANN	Benign	0.72
PhyloP100		-0.36
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: rs9472414; hg19: chr6-44946506;