Variant chr19-39464893-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001111020.3(SUPT5H):c.720G>A(p.Glu240=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 1,614,046 control chromosomes in the GnomAD database, including 23,302 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2046 hom., cov: 32)

Exomes 𝑓: 0.17 ( 21256 hom. )

Consequence

SUPT5H
NM_001111020.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.44

Variant links:

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]

SUPT5H links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 19-39464893-G-A is Benign according to our data. Variant chr19-39464893-G-A is described in ClinVar as [Benign]. Clinvar id is 1256822.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUPT5H	NM_001111020.3 linkuse as main transcript	c.720G>A	p.Glu240=	synonymous_variant	11/30	ENST00000432763.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUPT5H	ENST00000432763.7 linkuse as main transcript	c.720G>A	p.Glu240=	synonymous_variant	11/30	1	NM_001111020.3	P1	O00267-1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24535

AN:

152056

Hom.:

2046

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.146

AC:

36808

AN:

251420

Hom.:

2832

AF XY:

0.146

AC XY:

19804

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.113

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.0989

Gnomad SAS exome

AF:

0.108

Gnomad FIN exome

AF:

0.179

Gnomad NFE exome

AF:

0.168

Gnomad OTH exome

AF:

0.149

GnomAD4 exome

AF:

0.168

AC:

245590

AN:

1461872

Hom.:

21256

Cov.:

AF XY:

0.167

AC XY:

121257

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.118

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.0934

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.179

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.161

AC:

24530

AN:

152174

Hom.:

2046

Cov.:

AF XY:

0.160

AC XY:

11879

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.112

Gnomad4 FIN

AF:

0.180

Gnomad4 NFE

AF:

0.175

Gnomad4 OTH

AF:

0.147

Alfa

AF:

0.161

Hom.:

3376

Bravo

AF:

0.155

Asia WGS

AF:

0.126

AC:

442

AN:

3478

EpiCase

AF:

0.165

EpiControl

AF:

0.167

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 24, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

8.2

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over