Genetic Variant SUPT20HL1:p.Ala511_Ala517del (chrX-24364256-TTGCTGCTGCTGCTGCTGCTGC-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.1531_1551delGCTGCTGCTGCTGCTGCTGCT(p.Ala511_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 0.000294 in 803,852 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 73 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 0.00083 ( 0 hom., 19 hem., cov: 2)

Exomes 𝑓: 0.00023 ( 0 hom. 54 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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001136234.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 19 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.1531_1551delGCTGCTGCTGCTGCTGCTGCT	p.Ala511_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.1531_1551delGCTGCTGCTGCTGCTGCTGCT	p.Ala511_Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1531_1551delGCTGCTGCTGCTGCTGCTGCT	p.Ala511_Ala517del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.000840

AC:

AN:

82141

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000924

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000512

Gnomad ASJ

AF:

0.00146

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000805

Gnomad OTH

AF:

0.00281

GnomAD4 exome

AF:

0.000233

AC:

168

AN:

721703

Hom.:

AF XY:

0.000240

AC XY:

AN XY:

225403

show subpopulations

African (AFR)

AF:

0.000193

AC:

AN:

15560

American (AMR)

AF:

0.000299

AC:

AN:

26739

Ashkenazi Jewish (ASJ)

AF:

0.00127

AC:

AN:

15750

East Asian (EAS)

AF:

0.000443

AC:

AN:

24823

South Asian (SAS)

AF:

0.000290

AC:

AN:

41330

European-Finnish (FIN)

AF:

0.0000553

AC:

AN:

36141

Middle Eastern (MID)

AF:

0.000304

AC:

AN:

3289

European-Non Finnish (NFE)

AF:

0.000192

AC:

101

AN:

525442

Other (OTH)

AF:

0.000306

AC:

AN:

32629

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.434

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.000828

AC:

AN:

82149

Hom.:

Cov.:

AF XY:

0.000984

AC XY:

AN XY:

19301

show subpopulations

African (AFR)

AF:

0.000864

AC:

AN:

17357

American (AMR)

AF:

0.000511

AC:

AN:

7825

Ashkenazi Jewish (ASJ)

AF:

0.00146

AC:

AN:

2061

East Asian (EAS)

AF:

0.00251

AC:

AN:

2789

South Asian (SAS)

AF:

0.00

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:

0.000805

AC:

AN:

44734

Other (OTH)

AF:

0.00277

AC:

AN:

1084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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X-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGC

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