6-45276678-T-C

Variant names:

• chr6-45276678-T-C
• rs10948222
• NM_003599.4:c.101+88523A>G

Variant summary

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

The NM_003599.4(SUPT3H):​c.101+88523A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,098 control chromosomes in the GnomAD database, including 12,704 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 0.40 (12704 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.101+88523A>G		intron_variant	Intron 2 of 10	ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.101+88523A>G		intron_variant	Intron 2 of 10	1	NM_003599.4	ENSP00000360514.1
SUPT3H	ENST00000371460.5	c.134+45118A>G		intron_variant	Intron 4 of 12	1		ENSP00000360515.1
SUPT3H	ENST00000459689.1	n.215-25542A>G		intron_variant	Intron 2 of 2	2
SUPT3H	ENST00000475057.5	n.101+88523A>G		intron_variant	Intron 2 of 11	2		ENSP00000436411.1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61071 AN: 151980 Hom.: 12689 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.402 AC: 61109 AN: 152098 Hom.: 12704 Cov.: 32 AF XY: 0.403 AC XY: 29935 AN XY: 74356

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.425

Alfa AF: 0.411 Hom.: 6314

Bravo AF: 0.396

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.77

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: rs10948222; hg19: chr6-45244415;