Genetic Variant SUPT20HL1:p.Ala508_Ala517del (chrX-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-T) – 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.1522_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT(p.Ala508_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 0.0000286 in 803,974 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. It is difficult to determine the true allele frequency of this variant because it is of type DEL_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 0.00013 ( 0 hom., 4 hem., cov: 2)

Exomes 𝑓: 0.000017 ( 0 hom. 4 hem. )

Consequence

SUPT20HL1
NM_001136234.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.439

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 4 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.1522_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT	p.Ala508_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.1522_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT	p.Ala508_Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1522_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT	p.Ala508_Ala517del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.000134

AC:

AN:

82146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000462

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000719

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000447

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000166

AC:

AN:

721820

Hom.:

AF XY:

0.0000177

AC XY:

AN XY:

225478

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15567

American (AMR)

AF:

0.0000748

AC:

AN:

26742

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15764

East Asian (EAS)

AF:

0.0000403

AC:

AN:

24830

South Asian (SAS)

AF:

0.0000967

AC:

AN:

41346

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36142

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3290

European-Non Finnish (NFE)

AF:

0.00000951

AC:

AN:

525497

Other (OTH)

AF:

0.00

AC:

AN:

32642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.413

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

AF:

0.000134

AC:

AN:

82154

Hom.:

Cov.:

AF XY:

0.000207

AC XY:

AN XY:

19302

show subpopulations

African (AFR)

AF:

0.000461

AC:

AN:

17360

American (AMR)

AF:

0.00

AC:

AN:

7825

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2061

East Asian (EAS)

AF:

0.00

AC:

AN:

2792

South Asian (SAS)

AF:

0.000728

AC:

AN:

1373

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4177

Middle Eastern (MID)

AF:

0.00

AC:

AN:

183

European-Non Finnish (NFE)

AF:

0.0000447

AC:

AN:

44733

Other (OTH)

AF:

0.00

AC:

AN:

1084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.432

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

Alfa

AF:

0.00

Hom.:

142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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X-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGC

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