Genetic Variant SUPT20HL1:p.Ala516_Ala517del (chrX-24364256-TTGCTGC-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP3BP6BS1BS2

The NM_001136234.3(SUPT20HL1):c.1546_1551delGCTGCT(p.Ala516_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 0.00508 in 797,577 control chromosomes in the GnomAD database, including 34 homozygotes. There are 829 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.011 ( 18 hom., 243 hem., cov: 2)

Exomes 𝑓: 0.0044 ( 16 hom. 586 hem. )

Consequence

SUPT20HL1
NM_001136234.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:2

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 -10 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001136234.3

BP6

Variant X-24364256-TTGCTGC-T is Benign according to our data. Variant chrX-24364256-TTGCTGC-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1206090.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0112 (917/82108) while in subpopulation AFR AF = 0.0268 (464/17332). AF 95% confidence interval is 0.0248. There are 18 homozygotes in GnomAd4. There are 243 alleles in the male GnomAd4 subpopulation. Median coverage is 2. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 18 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.1546_1551delGCTGCT	p.Ala516_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.1546_1551delGCTGCT	p.Ala516_Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1546_1551delGCTGCT	p.Ala516_Ala517del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes

AF:

0.0112

AC:

918

AN:

82102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0268

Gnomad AMI

AF:

0.00353

Gnomad AMR

AF:

0.00473

Gnomad ASJ

AF:

0.00970

Gnomad EAS

AF:

0.00464

Gnomad SAS

AF:

0.00864

Gnomad FIN

AF:

0.0300

Gnomad MID

AF:

0.0100

Gnomad NFE

AF:

0.00514

Gnomad OTH

AF:

0.0131

GnomAD4 exome

AF:

0.00438

AC:

3132

AN:

715469

Hom.:

AF XY:

0.00266

AC XY:

586

AN XY:

219963

show subpopulations

African (AFR)

AF:

0.0160

AC:

246

AN:

15362

American (AMR)

AF:

0.00358

AC:

AN:

26537

Ashkenazi Jewish (ASJ)

AF:

0.00647

AC:

101

AN:

15615

East Asian (EAS)

AF:

0.00819

AC:

194

AN:

23699

South Asian (SAS)

AF:

0.00499

AC:

194

AN:

38907

European-Finnish (FIN)

AF:

0.0234

AC:

836

AN:

35788

Middle Eastern (MID)

AF:

0.00705

AC:

AN:

3262

European-Non Finnish (NFE)

AF:

0.00241

AC:

1265

AN:

523905

Other (OTH)

AF:

0.00549

AC:

178

AN:

32394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.434

Heterozygous variant carriers

145

289

434

578

723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.0112

AC:

917

AN:

82108

Hom.:

Cov.:

AF XY:

0.0126

AC XY:

243

AN XY:

19284

show subpopulations

African (AFR)

AF:

0.0268

AC:

464

AN:

17332

American (AMR)

AF:

0.00473

AC:

AN:

7825

Ashkenazi Jewish (ASJ)

AF:

0.00970

AC:

AN:

2061

East Asian (EAS)

AF:

0.00430

AC:

AN:

2792

South Asian (SAS)

AF:

0.00802

AC:

AN:

1372

European-Finnish (FIN)

AF:

0.0300

AC:

125

AN:

4166

Middle Eastern (MID)

AF:

0.0109

AC:

AN:

183

European-Non Finnish (NFE)

AF:

0.00514

AC:

230

AN:

44727

Other (OTH)

AF:

0.0129

AC:

AN:

1084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

121

151

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:

0.00966

Hom.:

142

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

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