NM_003599.4:c.*1253A>G

Variant names:

• chr6-44828563-T-C
• rs9472374
• NM_003599.4:c.*1253A>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.*1253A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,192 control chromosomes in the GnomAD database, including 962 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 0.087 (962 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 1 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]

ENSG00000286417 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.*1253A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.*1253A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_003599.4	ENSP00000360514.1

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13275 AN: 152074 Hom.: 961 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.0361

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0874 AC: 13298 AN: 152192 Hom.: 962 Cov.: 32 AF XY: 0.0878 AC XY: 6535 AN XY: 74408

African (AFR) AF: 0.195 AC: 8114 AN: 41514

American (AMR) AF: 0.0961 AC: 1468 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0361 AC: 125 AN: 3464

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5190

South Asian (SAS) AF: 0.0634 AC: 306 AN: 4824

European-Finnish (FIN) AF: 0.0682 AC: 724 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2353 AN: 67996

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0605 Hom.: 161

Bravo AF: 0.0946

Asia WGS AF: 0.0420 AC: 147 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.85
PhyloP100		-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9472374; hg19: chr6-44796300;