Genetic Variant SUPT5H:c.308-155G>A (chr19-39458139-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230

Publications

9 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001111020.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SUPT5H	NM_001111020.3	MANE Select	c.308-155G>A	intron	N/A	NP_001104490.1
SUPT5H	NM_001130824.2		c.308-155G>A	intron	N/A	NP_001124296.1
SUPT5H	NM_001319990.2		c.308-155G>A	intron	N/A	NP_001306919.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SUPT5H	ENST00000432763.7	TSL:1 MANE Select	c.308-155G>A	intron	N/A	ENSP00000404029.4
SUPT5H	ENST00000598725.5	TSL:1	c.308-155G>A	intron	N/A	ENSP00000469090.1
SUPT5H	ENST00000359191.10	TSL:1	c.307+399G>A	intron	N/A	ENSP00000352117.6

Frequencies

GnomAD3 genomes

AF:

0.462

AC:

69812

AN:

151052

Hom.:

18014

Cov.:

show subpopulations

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.:

AF XY:

0.358

AC XY:

201560

AN XY:

562730

show subpopulations

African (AFR)

AF:

0.715

AC:

18101

AN:

25316

American (AMR)

AF:

0.348

AC:

8620

AN:

24780

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

6698

AN:

18822

East Asian (EAS)

AF:

0.499

AC:

17160

AN:

34400

South Asian (SAS)

AF:

0.344

AC:

21820

AN:

63500

European-Finnish (FIN)

AF:

0.392

AC:

12159

AN:

31038

Middle Eastern (MID)

AF:

0.410

AC:

1374

AN:

3350

European-Non Finnish (NFE)

AF:

0.341

AC:

304131

AN:

891664

Other (OTH)

AF:

0.387

AC:

18885

AN:

48818

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

12488

24977

37465

49954

62442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9558

19116

28674

38232

47790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.462

AC:

69900

AN:

151170

Hom.:

18051

Cov.:

AF XY:

0.461

AC XY:

34026

AN XY:

73788

show subpopulations

African (AFR)

AF:

0.705

AC:

28986

AN:

41098

American (AMR)

AF:

0.378

AC:

5737

AN:

15176

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1229

AN:

3466

East Asian (EAS)

AF:

0.516

AC:

2634

AN:

5100

South Asian (SAS)

AF:

0.365

AC:

1750

AN:

4790

European-Finnish (FIN)

AF:

0.405

AC:

4229

AN:

10450

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.354

AC:

24016

AN:

67784

Other (OTH)

AF:

0.447

AC:

941

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1674

3348

5022

6696

8370

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

618

1236

1854

2472

3090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.431

Hom.:

11925

Bravo

AF:

0.469

Asia WGS

AF:

0.508

AC:

1767

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

-0.023

PromoterAI

-0.069

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over