dbSNP rs11881477: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUPT5H	NM_001111020.3 link	c.308-155G>A		intron_variant	Intron 4 of 29	ENST00000432763.7	NP_001104490.1	O00267-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT5H	ENST00000432763.7 link	c.308-155G>A		intron_variant	Intron 4 of 29	1	NM_001111020.3	ENSP00000404029.4		O00267-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over