rs9395049

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-44824981-A-G
• chr6-44824981-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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	ENST00000671451.1	n.160-4607A>G		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.536

Alfa AF: 0.471 Hom.: 5671

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9395049; hg19: chr6-44792718;