X-24364256-TTGCTGCTGCTGCTGC-T

Variant names:

• chrX-24364256-TTGCTGCTGCTGCTGC-T
• rs35206911
• NM_001136234.3:c.1537_1551delGCTGCTGCTGCTGCT

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

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
• Clinical Significance: Uncertain significance no assertion criteria provided U:2
• Conservation: PhyloP100: 0.439

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]

ACMG classification

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
SUPT20HL1	NM_001136234.3	c.1537_1551delGCTGCTGCTGCTGCT	p.Ala513_Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENST00000686983.1	NP_001129706.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUPT20HL1	ENST00000686983.1	c.1537_1551delGCTGCTGCTGCTGCT	p.Ala513_Ala517del	conservative_inframe_deletion	Exon 1 of 1		NM_001136234.3	ENSP00000509731.1
SUPT20HL1	ENST00000436466.2	c.1537_1551delGCTGCTGCTGCTGCT	p.Ala513_Ala517del	conservative_inframe_deletion	Exon 2 of 2	6		ENSP00000502907.1

Frequencies

GnomAD3 genomes AF: 0.00403 AC: 331 AN: 82140 Hom.: 0 Cov.: 2 AF XY: 0.00441 AC XY: 85 AN XY: 19276

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

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

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

Submissions by phenotype

not provided Uncertain:2

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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

- -

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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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35206911; hg19: chrX-24382373;