rs9472409

Positions:

• chr6-44958694-A-G
• chr6-44958694-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003599.4(SUPT3H):​c.580+3059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,706 control chromosomes in the GnomAD database, including 16,334 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 0.46 (16334 hom., cov: 29)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

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

Verdict is Benign. Variant got -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 = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUPT3H	NM_003599.4	c.580+3059T>C		intron_variant		ENST00000371459.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUPT3H	ENST00000371459.6	c.580+3059T>C		intron_variant		1	NM_003599.4	P1
SUPT3H	ENST00000371460.5	c.613+3059T>C		intron_variant		1
SUPT3H	ENST00000637763.2	c.394+3059T>C		intron_variant		3
SUPT3H	ENST00000475057.5	c.580+3059T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69275 AN: 151588 Hom.: 16318 Cov.: 29

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.457 AC: 69326 AN: 151706 Hom.: 16334 Cov.: 29 AF XY: 0.459 AC XY: 33982 AN XY: 74104

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.473

Alfa AF: 0.478 Hom.: 8124

Bravo AF: 0.459

Asia WGS AF: 0.333 AC: 1159 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	2.7
DANN	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs9472409; hg19: chr6-44926431;