rs11881477

Positions:

• chr19-39458139-G-A
• chr19-39458139-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001111020.3(SUPT5H):​c.308-155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,292,858 control chromosomes in the GnomAD database, including 97,215 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 (18051 hom., cov: 28)
  • Exomes 𝑓: 0.36 (79164 hom.)
• Consequence: SUPT5H NM_001111020.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

SUPT5H (HGNC:11469): (SPT5 homolog, DSIF elongation factor subunit) Enables enzyme binding activity and protein heterodimerization activity. Involved in positive regulation of macroautophagy; regulation of RNA metabolic process; and transcription elongation from RNA polymerase II promoter. Located in nucleoplasm. Part of DSIF complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUPT5H	NM_001111020.3	c.308-155G>A		intron_variant		ENST00000432763.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUPT5H	ENST00000432763.7	c.308-155G>A		intron_variant		1	NM_001111020.3	P1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 69812 AN: 151052 Hom.: 18014 Cov.: 28

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.445

GnomAD4 exome AF: 0.358 AC: 408948 AN: 1141688 Hom.: 79164 Cov.: 17 AF XY: 0.358 AC XY: 201560 AN XY: 562730

Gnomad4 AFR exome AF: 0.715

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.356

Gnomad4 EAS exome AF: 0.499

Gnomad4 SAS exome AF: 0.344

Gnomad4 FIN exome AF: 0.392

Gnomad4 NFE exome AF: 0.341

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.462 AC: 69900 AN: 151170 Hom.: 18051 Cov.: 28 AF XY: 0.461 AC XY: 34026 AN XY: 73788

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.447

Alfa AF: 0.381 Hom.: 5470

Bravo AF: 0.469

Asia WGS AF: 0.508 AC: 1767 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	16
DANN	Benign	0.83

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: rs11881477; hg19: chr19-39948779;