6-44999753-T-C

Position:

• chr6-44999753-T-C

Variant summary

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

The NM_003599.4(SUPT3H):​c.504+3900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,904 control chromosomes in the GnomAD database, including 9,862 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 0.35 (9862 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUPT3H	NM_003599.4	c.504+3900A>G		intron_variant		ENST00000371459.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUPT3H	ENST00000371459.6	c.504+3900A>G		intron_variant		1	NM_003599.4	P1
SUPT3H	ENST00000371460.5	c.537+3900A>G		intron_variant		1
SUPT3H	ENST00000637763.2	c.318+3900A>G		intron_variant		3
SUPT3H	ENST00000475057.5	c.504+3900A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53010 AN: 151786 Hom.: 9849 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.349 AC: 53053 AN: 151904 Hom.: 9862 Cov.: 32 AF XY: 0.351 AC XY: 26084 AN XY: 74218

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.361

Alfa AF: 0.403 Hom.: 18380

Bravo AF: 0.347

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.71

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: rs10948197; hg19: chr6-44967490;