Genetic Variant SUPT20HL1:p.Ala513_Ala517dup (chrX-24364256-T-TTGCTGCTGCTGCTGC) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2

The NM_001136234.3(SUPT20HL1):c.1537_1551dupGCTGCTGCTGCTGCT(p.Ala513_Ala517dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., 49 hem., cov: 2)

Exomes 𝑓: 0.0027 ( 44 hom. 391 hem. )

Failed GnomAD Quality Control

Consequence

SUPT20HL1
NM_001136234.3 conservative_inframe_insertion

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: Likely_benign. The variant received -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001136234.3

BS2

High Hemizygotes in GnomAd4 at 49 gene

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.1537_1551dupGCTGCTGCTGCTGCT	p.Ala513_Ala517dup	conservative_inframe_insertion	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.1537_1551dupGCTGCTGCTGCTGCT	p.Ala513_Ala517dup	conservative_inframe_insertion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1537_1551dupGCTGCTGCTGCTGCT	p.Ala513_Ala517dup	conservative_inframe_insertion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.00282

AC:

232

AN:

82135

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00185

Gnomad AMI

AF:

0.00177

Gnomad AMR

AF:

0.00358

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00357

Gnomad SAS

AF:

0.0101

Gnomad FIN

AF:

0.000958

Gnomad MID

AF:

0.00500

Gnomad NFE

AF:

0.00315

Gnomad OTH

AF:

0.000936

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00275

AC:

1980

AN:

720676

Hom.:

Cov.:

AF XY:

0.00174

AC XY:

391

AN XY:

224544

show subpopulations

African (AFR)

AF:

0.00219

AC:

AN:

15546

American (AMR)

AF:

0.00292

AC:

AN:

26687

Ashkenazi Jewish (ASJ)

AF:

0.000190

AC:

AN:

15762

East Asian (EAS)

AF:

0.00194

AC:

AN:

24783

South Asian (SAS)

AF:

0.00485

AC:

199

AN:

41024

European-Finnish (FIN)

AF:

0.00150

AC:

AN:

36116

Middle Eastern (MID)

AF:

0.00640

AC:

AN:

3279

European-Non Finnish (NFE)

AF:

0.00273

AC:

1434

AN:

524890

Other (OTH)

AF:

0.00334

AC:

109

AN:

32589

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

130

195

260

325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.00284

AC:

233

AN:

82143

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

AN XY:

19301

show subpopulations

African (AFR)

AF:

0.00190

AC:

AN:

17356

American (AMR)

AF:

0.00358

AC:

AN:

7825

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2061

East Asian (EAS)

AF:

0.00358

AC:

AN:

2792

South Asian (SAS)

AF:

0.0102

AC:

AN:

1371

European-Finnish (FIN)

AF:

0.000958

AC:

AN:

4177

Middle Eastern (MID)

AF:

0.00546

AC:

AN:

183

European-Non Finnish (NFE)

AF:

0.00315

AC:

141

AN:

44728

Other (OTH)

AF:

0.000923

AC:

AN:

1084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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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X-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC

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