chr6-44869619-T-G

Variant names:

• chr6-44869619-T-G
• rs3799977
• NM_003599.4:c.913-39762A>C

Variant summary

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

The NM_003599.4(SUPT3H):​c.913-39762A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,946 control chromosomes in the GnomAD database, including 9,530 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 0.34 (9530 hom., cov: 32)
• Consequence: SUPT3H NM_003599.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 23 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT3H	NM_003599.4	c.913-39762A>C		intron_variant	Intron 10 of 10	ENST00000371459.6	NP_003590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT3H	ENST00000371459.6	c.913-39762A>C		intron_variant	Intron 10 of 10	1	NM_003599.4	ENSP00000360514.1
SUPT3H	ENST00000371460.5	c.946-39762A>C		intron_variant	Intron 12 of 12	1		ENSP00000360515.1
SUPT3H	ENST00000371458.1	c.262-39743A>C		intron_variant	Intron 4 of 4	5		ENSP00000360513.1
SUPT3H	ENST00000475057.5	n.913-39762A>C		intron_variant	Intron 10 of 11	2		ENSP00000436411.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51041 AN: 151828 Hom.: 9518 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.336 AC: 51074 AN: 151946 Hom.: 9530 Cov.: 32 AF XY: 0.339 AC XY: 25147 AN XY: 74278

African (AFR) AF: 0.163 AC: 6742 AN: 41440

American (AMR) AF: 0.415 AC: 6331 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1456 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1534 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4812

European-Finnish (FIN) AF: 0.415 AC: 4371 AN: 10526

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28051 AN: 67948

Other (OTH) AF: 0.356 AC: 751 AN: 2110

Alfa AF: 0.378 Hom.: 26727

Bravo AF: 0.332

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.24
DANN	Benign	0.62
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3799977; hg19: chr6-44837356;