19-39436900-C-T

Variant names:

• chr19-39436900-C-T
• rs530411
• ENST00000594990.5:c.-375+723C>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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT5H	ENST00000594990.5	c.-375+723C>T		intron_variant	Intron 1 of 5	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;