GeneBe

rs35206911

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001136234.3(SUPT20HL1):​c.1513_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT​(p.Ala505_Ala517del) variant causes a conservative inframe deletion 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 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: not found (cov: 2)
Exomes 𝑓: 0.0000014 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control

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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001136234.3

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.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SUPT20HL1
NM_001136234.3
MANE Select
c.1513_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTp.Ala505_Ala517del
conservative_inframe_deletion
Exon 1 of 1NP_001129706.3A0A7I2YQ69

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SUPT20HL1
ENST00000686983.1
MANE Select
c.1513_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTp.Ala505_Ala517del
conservative_inframe_deletion
Exon 1 of 1ENSP00000509731.1A0A7I2YQ69
SUPT20HL1
ENST00000436466.2
TSL:6
c.1513_1551delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTp.Ala505_Ala517del
conservative_inframe_deletion
Exon 2 of 2ENSP00000502907.1A0A7I2YQ69

Frequencies

GnomAD3 genomes
Cov.:
2
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000139
AC:
1
AN:
721827
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
225485
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
15567
American (AMR)
AF:
0.00
AC:
0
AN:
26742
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15764
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24830
South Asian (SAS)
AF:
0.00
AC:
0
AN:
41346
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36142
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3290
European-Non Finnish (NFE)
AF:
0.00000190
AC:
1
AN:
525503
Other (OTH)
AF:
0.00
AC:
0
AN:
32643
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
2
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

Other links and lift over

dbSNP: rs35206911; hg19: chrX-24382373; API