Genetic Variant SUPT20HL1:p.Ala515_Ala517del (chrX-24364256-TTGCTGCTGC-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3BA1

The NM_001136234.3(SUPT20HL1):c.1543_1551delGCTGCTGCT(p.Ala515_Ala517del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00618 in 802,189 control chromosomes in the GnomAD database, including 115 homozygotes. There are 1,148 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.019 ( 52 hom., 373 hem., cov: 2)

Exomes 𝑓: 0.0047 ( 63 hom. 775 hem. )

Consequence

SUPT20HL1
NM_001136234.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334

Publications

1 publications found

Variant links:

Genes affected

SUPT20HL1 (HGNC:30773): (SUPT20H like 1) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of SAGA complex. [provided by Alliance of Genome Resources, Apr 2022]

SUPT20HL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001136234.3

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136234.3. 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
	SUPT20HL1	NM_001136234.3	MANE Select	c.1543_1551delGCTGCTGCT	p.Ala515_Ala517del	conservative_inframe_deletion	Exon 1 of 1	NP_001129706.3	A0A7I2YQ69

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUPT20HL1	ENST00000686983.1	MANE Select	c.1543_1551delGCTGCTGCT	p.Ala515_Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1543_1551delGCTGCTGCT	p.Ala515_Ala517del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.0189

AC:

1555

AN:

82106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0642

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.0104

Gnomad ASJ

AF:

0.000485

Gnomad EAS

AF:

0.0440

Gnomad SAS

AF:

0.00432

Gnomad FIN

AF:

0.000479

Gnomad MID

AF:

0.0300

Gnomad NFE

AF:

0.00308

Gnomad OTH

AF:

0.0150

GnomAD4 exome

AF:

0.00472

AC:

3400

AN:

720076

Hom.:

AF XY:

0.00346

AC XY:

775

AN XY:

224024

show subpopulations

African (AFR)

AF:

0.0395

AC:

608

AN:

15406

American (AMR)

AF:

0.00649

AC:

173

AN:

26659

Ashkenazi Jewish (ASJ)

AF:

0.000445

AC:

AN:

15734

East Asian (EAS)

AF:

0.0677

AC:

1654

AN:

24432

South Asian (SAS)

AF:

0.00263

AC:

108

AN:

41034

European-Finnish (FIN)

AF:

0.00106

AC:

AN:

35955

Middle Eastern (MID)

AF:

0.00791

AC:

AN:

3285

European-Non Finnish (NFE)

AF:

0.00113

AC:

595

AN:

525018

Other (OTH)

AF:

0.00587

AC:

191

AN:

32553

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.405

Heterozygous variant carriers

119

238

356

475

594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.0190

AC:

1557

AN:

82113

Hom.:

Cov.:

AF XY:

0.0193

AC XY:

373

AN XY:

19293

show subpopulations

African (AFR)

AF:

0.0642

AC:

1113

AN:

17331

American (AMR)

AF:

0.0104

AC:

AN:

7823

Ashkenazi Jewish (ASJ)

AF:

0.000485

AC:

AN:

2061

East Asian (EAS)

AF:

0.0441

AC:

123

AN:

2786

South Asian (SAS)

AF:

0.00437

AC:

AN:

1373

European-Finnish (FIN)

AF:

0.000479

AC:

AN:

4177

Middle Eastern (MID)

AF:

0.0328

AC:

AN:

183

European-Non Finnish (NFE)

AF:

0.00309

AC:

138

AN:

44729

Other (OTH)

AF:

0.0148

AC:

AN:

1084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

120

160

200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00

Hom.:

142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.33

Splicing

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