chr17-72120678-T-TGC

Variant names:

• chr17-72120678-T-TGC
• rs112088991
• ENST00000533232.5:n.31+84_31+85insGC

Variant summary

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

The ENST00000533232.5(SOX9-AS1):​n.31+84_31+85insGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 150,926 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 0.00081 (0 hom., cov: 31)
  • Exomes 𝑓: 0.026 (0 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• 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+83_31+84dupGC		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000533232.5	TSL:1	n.31+84_31+85insGC		intron	N/A
	SOX9-AS1	ENST00000414600.1	TSL:3	n.96+21006_96+21007insGC		intron	N/A
	ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35634_147-35633insGC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000806 AC: 120 AN: 148894 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000246

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00250

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00602

Gnomad SAS AF: 0.000847

Gnomad FIN AF: 0.000294

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000538

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0264 AC: 51 AN: 1934 Hom.: 0 AF XY: 0.0241 AC XY: 22 AN XY: 914

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 94

American (AMR) AF: 0.0667 AC: 2 AN: 30

Ashkenazi Jewish (ASJ) AF: 0.0227 AC: 4 AN: 176

East Asian (EAS) AF: 0.0417 AC: 15 AN: 360

South Asian (SAS) AF: 0.0714 AC: 2 AN: 28

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14

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

European-Non Finnish (NFE) AF: 0.0241 AC: 26 AN: 1078

Other (OTH) AF: 0.0139 AC: 2 AN: 144

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000805 AC: 120 AN: 148992 Hom.: 0 Cov.: 31 AF XY: 0.00109 AC XY: 79 AN XY: 72658

African (AFR) AF: 0.000245 AC: 10 AN: 40748

American (AMR) AF: 0.00250 AC: 37 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3408

East Asian (EAS) AF: 0.00604 AC: 30 AN: 4966

South Asian (SAS) AF: 0.000848 AC: 4 AN: 4718

European-Finnish (FIN) AF: 0.000294 AC: 3 AN: 10210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.000538 AC: 36 AN: 66892

Other (OTH) AF: 0.00 AC: 0 AN: 2066

Alfa AF: 0.000109 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs112088991; hg19: chr17-70116819;