rs10948172

chr6-44809954-A-G

Variant summary

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

The ENST00000671451.1(ENSG00000286417):n.160-19634A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,070 control chromosomes in the GnomAD database, including 5,808 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 0.27 (5808 hom., cov: 32)
• Consequence: ENST00000671451.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

(HGNC:):

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929770	XR_926855.3	n.246-19634A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671451.1	n.160-19634A>G		intron_variant, non_coding_transcript_variant
SUPT3H	ENST00000475057.5	c.*53-453T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40908 AN: 151952 Hom.: 5798 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.269 AC: 40938 AN: 152070 Hom.: 5808 Cov.: 32 AF XY: 0.266 AC XY: 19794 AN XY: 74314

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0384

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.251

Alfa AF: 0.277 Hom.: 12129

Bravo AF: 0.264

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10948172; hg19: chr6-44777691;