X-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC

Variant names:

• chrX-24364256-TTGC-T
• rs35206911
• NM_001136234.3:c.1549_1551delGCT

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3 BA1

The NM_001136234.3(SUPT20HL1):​c.1549_1551delGCT​(p.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 0.0372 in 743,181 control chromosomes in the GnomAD database, including 494 homozygotes. There are 4,045 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.035 (101 hom., 663 hem., cov: 2)
  • Exomes 𝑓: 0.037 (393 hom. 3382 hem.)
• Consequence: SUPT20HL1 NM_001136234.3 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -9 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001136234.3
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

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.1549_1551delGCT	p.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.1549_1551delGCT	p.Ala517del	conservative_inframe_deletion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1549_1551delGCT	p.Ala517del	conservative_inframe_deletion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 2912 AN: 82060 Hom.: 101 Cov.: 2

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0601

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0316

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0452

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0403

GnomAD4 exome AF: 0.0374 AC: 24726 AN: 661114 Hom.: 393 AF XY: 0.0175 AC XY: 3382 AN XY: 193382

African (AFR) AF: 0.0646 AC: 973 AN: 15063

American (AMR) AF: 0.0290 AC: 723 AN: 24918

Ashkenazi Jewish (ASJ) AF: 0.0459 AC: 659 AN: 14350

East Asian (EAS) AF: 0.151 AC: 3233 AN: 21366

South Asian (SAS) AF: 0.0704 AC: 2569 AN: 36505

European-Finnish (FIN) AF: 0.0274 AC: 906 AN: 33074

Middle Eastern (MID) AF: 0.0619 AC: 192 AN: 3102

European-Non Finnish (NFE) AF: 0.0291 AC: 14078 AN: 483253

Other (OTH) AF: 0.0472 AC: 1393 AN: 29483

GnomAD4 genome AF: 0.0355 AC: 2913 AN: 82067 Hom.: 101 Cov.: 2 AF XY: 0.0344 AC XY: 663 AN XY: 19289

African (AFR) AF: 0.0516 AC: 894 AN: 17330

American (AMR) AF: 0.0403 AC: 315 AN: 7823

Ashkenazi Jewish (ASJ) AF: 0.0316 AC: 65 AN: 2055

East Asian (EAS) AF: 0.156 AC: 432 AN: 2777

South Asian (SAS) AF: 0.129 AC: 177 AN: 1371

European-Finnish (FIN) AF: 0.0257 AC: 107 AN: 4165

Middle Eastern (MID) AF: 0.0549 AC: 10 AN: 182

European-Non Finnish (NFE) AF: 0.0187 AC: 836 AN: 44716

Other (OTH) AF: 0.0397 AC: 43 AN: 1082

Alfa AF: 0.0404 Hom.: 142

ClinVar

Not reported in ClinVar

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

Other links and lift over

dbSNP: rs35206911; hg19: chrX-24382373;