X-24364256-TTGCTGCTGCTGCTGC-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_001136234.3(SUPT20HL1):​c.1537_1551delGCTGCTGCTGCTGCT​(p.Ala513_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 0.00162 in 803,251 control chromosomes in the GnomAD database, including 2 homozygotes. There are 381 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.0041 ( 0 hom., 87 hem., cov: 2)
Exomes 𝑓: 0.0013 ( 2 hom. 294 hem. )

Consequence

SUPT20HL1
NM_001136234.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:2

Conservation

PhyloP100: 0.439
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 made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001136234.3
BS2
High Hemizygotes in GnomAd4 at 87 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SUPT20HL1NM_001136234.3 linkc.1537_1551delGCTGCTGCTGCTGCT p.Ala513_Ala517del conservative_inframe_deletion Exon 1 of 1 ENST00000686983.1 NP_001129706.3 A0A7I2YQ69

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SUPT20HL1ENST00000686983.1 linkc.1537_1551delGCTGCTGCTGCTGCT p.Ala513_Ala517del conservative_inframe_deletion Exon 1 of 1 NM_001136234.3 ENSP00000509731.1 A0A7I2YQ69
SUPT20HL1ENST00000436466.2 linkc.1537_1551delGCTGCTGCTGCTGCT p.Ala513_Ala517del conservative_inframe_deletion Exon 2 of 2 6 ENSP00000502907.1 A0A7I2YQ69

Frequencies

GnomAD3 genomes
AF:
0.00403
AC:
331
AN:
82140
Hom.:
0
Cov.:
2
AF XY:
0.00441
AC XY:
85
AN XY:
19276
show subpopulations
Gnomad AFR
AF:
0.00283
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00320
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00107
Gnomad SAS
AF:
0.00935
Gnomad FIN
AF:
0.00575
Gnomad MID
AF:
0.00500
Gnomad NFE
AF:
0.00474
Gnomad OTH
AF:
0.00375
GnomAD4 exome
AF:
0.00134
AC:
966
AN:
721103
Hom.:
2
AF XY:
0.00131
AC XY:
294
AN XY:
224973
show subpopulations
Gnomad4 AFR exome
AF:
0.00122
Gnomad4 AMR exome
AF:
0.00262
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000242
Gnomad4 SAS exome
AF:
0.00307
Gnomad4 FIN exome
AF:
0.00258
Gnomad4 NFE exome
AF:
0.00112
Gnomad4 OTH exome
AF:
0.00181
GnomAD4 genome
AF:
0.00407
AC:
334
AN:
82148
Hom.:
0
Cov.:
2
AF XY:
0.00451
AC XY:
87
AN XY:
19300
show subpopulations
Gnomad4 AFR
AF:
0.00294
Gnomad4 AMR
AF:
0.00319
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00107
Gnomad4 SAS
AF:
0.00947
Gnomad4 FIN
AF:
0.00575
Gnomad4 NFE
AF:
0.00474
Gnomad4 OTH
AF:
0.00461

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

not provided Uncertain:2
-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35206911; hg19: chrX-24382373; API