X-24364256-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC

Variant names:

• chrX-24364256-T-TTGCTGCTGC
• rs35206911
• NM_001136234.3:c.1543_1551dupGCTGCTGCT

Variant summary

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

The NM_001136234.3(SUPT20HL1):​c.1543_1551dupGCTGCTGCT​(p.Ala515_Ala517dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.057 (170 hom., 997 hem., cov: 2)
  • Exomes 𝑓: 0.049 (968 hom. 6431 hem.)
  • Failed GnomAD Quality Control
• Consequence: SUPT20HL1 NM_001136234.3 conservative_inframe_insertion
• 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 (SAS) allele frequency at 95% confidence interval = 0.11 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.1543_1551dupGCTGCTGCT	p.Ala515_Ala517dup	conservative_inframe_insertion	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.1543_1551dupGCTGCTGCT	p.Ala515_Ala517dup	conservative_inframe_insertion	Exon 1 of 1	ENSP00000509731.1	A0A7I2YQ69
	SUPT20HL1	ENST00000436466.2	TSL:6	c.1543_1551dupGCTGCTGCT	p.Ala515_Ala517dup	conservative_inframe_insertion	Exon 2 of 2	ENSP00000502907.1	A0A7I2YQ69

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 4644 AN: 81965 Hom.: 169 Cov.: 2

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0248

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.0287

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0644

Gnomad MID AF: 0.0653

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0524

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0490 AC: 34599 AN: 706097 Hom.: 968 Cov.: 18 AF XY: 0.0304 AC XY: 6431 AN XY: 211583

African (AFR) AF: 0.0171 AC: 265 AN: 15462

American (AMR) AF: 0.0764 AC: 1963 AN: 25694

Ashkenazi Jewish (ASJ) AF: 0.0246 AC: 383 AN: 15584

East Asian (EAS) AF: 0.0544 AC: 1315 AN: 24164

South Asian (SAS) AF: 0.0671 AC: 2504 AN: 37307

European-Finnish (FIN) AF: 0.0570 AC: 2005 AN: 35183

Middle Eastern (MID) AF: 0.0437 AC: 141 AN: 3227

European-Non Finnish (NFE) AF: 0.0474 AC: 24530 AN: 517497

Other (OTH) AF: 0.0467 AC: 1493 AN: 31979

GnomAD4 genome AF: 0.0566 AC: 4639 AN: 81971 Hom.: 170 Cov.: 2 AF XY: 0.0518 AC XY: 997 AN XY: 19255

African (AFR) AF: 0.0162 AC: 281 AN: 17346

American (AMR) AF: 0.0776 AC: 604 AN: 7787

Ashkenazi Jewish (ASJ) AF: 0.0287 AC: 59 AN: 2059

East Asian (EAS) AF: 0.0664 AC: 185 AN: 2785

South Asian (SAS) AF: 0.125 AC: 171 AN: 1368

European-Finnish (FIN) AF: 0.0644 AC: 268 AN: 4161

Middle Eastern (MID) AF: 0.0604 AC: 11 AN: 182

European-Non Finnish (NFE) AF: 0.0669 AC: 2988 AN: 44635

Other (OTH) AF: 0.0535 AC: 58 AN: 1084

Alfa AF: 0.0420 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;