6-44824981-A-G

Variant names:

• chr6-44824981-A-G
• rs9395049
• ENST00000475057.5:n.*52+4783T>C

Variant summary

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

The ENST00000475057.5(SUPT3H):​n.*52+4783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,074 control chromosomes in the GnomAD database, including 21,208 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 0.52 (21208 hom., cov: 32)
• Consequence: SUPT3H ENST00000475057.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NR_146632.2	n.1173+4783T>C		intron_variant	Intron 11 of 11
SUPT3H	NR_146633.1	n.1165+4783T>C		intron_variant	Intron 11 of 11
SUPT3H	NR_146634.2	n.1159+4783T>C		intron_variant	Intron 11 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000475057.5	n.*52+4783T>C		intron_variant	Intron 11 of 11	2		ENSP00000436411.1
ENSG00000286417	ENST00000671451.2	n.196-4607A>G		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.275-4607A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79706 AN: 151956 Hom.: 21178 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.525 AC: 79773 AN: 152074 Hom.: 21208 Cov.: 32 AF XY: 0.527 AC XY: 39137 AN XY: 74332

African (AFR) AF: 0.574 AC: 23818 AN: 41484

American (AMR) AF: 0.489 AC: 7472 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3597 AN: 5166

South Asian (SAS) AF: 0.665 AC: 3205 AN: 4818

European-Finnish (FIN) AF: 0.498 AC: 5260 AN: 10566

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32849 AN: 67976

Other (OTH) AF: 0.536 AC: 1131 AN: 2110

Alfa AF: 0.478 Hom.: 7243

Bravo AF: 0.524

Asia WGS AF: 0.687 AC: 2388 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	1.3
DANN	Benign	0.72
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9395049; hg19: chr6-44792718;