19-39436900-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000594990.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT5H	ENST00000594990.5	TSL:5	c.-375+723C>T		intron	N/A	ENSP00000471561.1	M0R105

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

African (AFR) AF: 0.605 AC: 25045 AN: 41366

American (AMR) AF: 0.366 AC: 5585 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3464

East Asian (EAS) AF: 0.510 AC: 2627 AN: 5156

South Asian (SAS) AF: 0.386 AC: 1856 AN: 4806

European-Finnish (FIN) AF: 0.400 AC: 4221 AN: 10556

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23506 AN: 67944

Other (OTH) AF: 0.438 AC: 923 AN: 2108

Alfa AF: 0.376 Hom.: 11670

Bravo AF: 0.435

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		0.042

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs530411;

hg19: chr19-39927540;