19-39436900-C-T

Position:

• chr19-39436900-C-T

Variant summary

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

The ENST00000594990.5(SUPT5H):​c.-375+723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,846 control chromosomes in the GnomAD database, including 15,198 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 0.43 (15198 hom., cov: 30)
• Consequence: SUPT5H ENST00000594990.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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]

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39436900C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUPT5H	ENST00000594990.5	c.-375+723C>T		intron_variant		5		ENSP00000471561.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65415 AN: 151728 Hom.: 15175 Cov.: 30

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65480 AN: 151846 Hom.: 15198 Cov.: 30 AF XY: 0.432 AC XY: 32020 AN XY: 74200

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.438

Alfa AF: 0.368 Hom.: 7577

Bravo AF: 0.435

Asia WGS AF: 0.503 AC: 1749 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	4.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs530411; hg19: chr19-39927540;