17-72120683-GCACACACACA-GCACA

Variant names:

• chr17-72120683-GCACACA-G
• rs1555628892
• ENST00000533232.5:n.31+74_31+79delTGTGTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000533232.5(SOX9-AS1):​n.31+74_31+79delTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 151,036 control chromosomes in the GnomAD database, including 154 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.027 (150 hom., cov: 0)
  • Exomes 𝑓: 0.042 (4 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.52
• Publications: 0 publications found

Genes affected

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

ENSG00000288605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

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+74_31+79delTGTGTG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000533232.5	TSL:1	n.31+74_31+79delTGTGTG		intron	N/A
	SOX9-AS1	ENST00000414600.1	TSL:3	n.96+20996_96+21001delTGTGTG		intron	N/A
	ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35644_147-35639delTGTGTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4010 AN: 149018 Hom.: 148 Cov.: 0

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0355

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0356

GnomAD4 exome AF: 0.0415 AC: 80 AN: 1926 Hom.: 4 AF XY: 0.0346 AC XY: 31 AN XY: 896

African (AFR) AF: 0.0116 AC: 1 AN: 86

American (AMR) AF: 0.0417 AC: 2 AN: 48

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 14 AN: 162

East Asian (EAS) AF: 0.118 AC: 42 AN: 356

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: 0.0120 AC: 13 AN: 1084

Other (OTH) AF: 0.0548 AC: 8 AN: 146

GnomAD4 genome AF: 0.0269 AC: 4018 AN: 149110 Hom.: 150 Cov.: 0 AF XY: 0.0306 AC XY: 2222 AN XY: 72580

African (AFR) AF: 0.0142 AC: 580 AN: 40732

American (AMR) AF: 0.0964 AC: 1449 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 148 AN: 3444

East Asian (EAS) AF: 0.102 AC: 507 AN: 4972

South Asian (SAS) AF: 0.0199 AC: 93 AN: 4664

European-Finnish (FIN) AF: 0.0354 AC: 355 AN: 10016

Middle Eastern (MID) AF: 0.0350 AC: 10 AN: 286

European-Non Finnish (NFE) AF: 0.0111 AC: 746 AN: 67004

Other (OTH) AF: 0.0362 AC: 75 AN: 2074

Alfa AF: 0.00175 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.5
Mutation Taster		=97/3	polymorphism

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;