17-72120683-GCACACACACA-GCACACACACACACA

Variant names:

• chr17-72120683-G-GCACA
• rs1555628892
• ENST00000533232.5:n.31+79_31+80insTGTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000533232.5(SOX9-AS1):​n.31+79_31+80insTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000841 in 151,048 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00084 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00052 (0 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 0 publications found

Genes affected

SOX9-AS1 (HGNC:49321): (SOX9 antisense RNA 1)

ENSG00000288605 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533232.5. 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
	SOX9-AS1	NR_103737.1		n.31+76_31+79dupTGTG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000533232.5	TSL:1	n.31+79_31+80insTGTG		intron	N/A
	SOX9-AS1	ENST00000414600.1	TSL:3	n.96+21001_96+21002insTGTG		intron	N/A
	ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35639_147-35638insTGTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000845 AC: 126 AN: 149036 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000542

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000932

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000200

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.00195

GnomAD4 exome AF: 0.000521 AC: 1 AN: 1920 Hom.: 0 AF XY: 0.00112 AC XY: 1 AN XY: 892

African (AFR) AF: 0.00 AC: 0 AN: 86

American (AMR) AF: 0.00 AC: 0 AN: 46

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 162

East Asian (EAS) AF: 0.00 AC: 0 AN: 354

South Asian (SAS) AF: 0.00 AC: 0 AN: 18

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 10

European-Non Finnish (NFE) AF: 0.000924 AC: 1 AN: 1082

Other (OTH) AF: 0.00 AC: 0 AN: 146

GnomAD4 genome AF: 0.000845 AC: 126 AN: 149128 Hom.: 0 Cov.: 0 AF XY: 0.000882 AC XY: 64 AN XY: 72594

African (AFR) AF: 0.000540 AC: 22 AN: 40738

American (AMR) AF: 0.000931 AC: 14 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3444

East Asian (EAS) AF: 0.000201 AC: 1 AN: 4976

South Asian (SAS) AF: 0.00193 AC: 9 AN: 4664

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10016

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.00113 AC: 76 AN: 67006

Other (OTH) AF: 0.00193 AC: 4 AN: 2076

Alfa AF: 0.000260 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1555628892; hg19: chr17-70116824;