chr17-72102020-G-C

Variant names:

• chr17-72102020-G-C
• rs9913711
• ENST00000533232.5:n.32-17992C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533232.5(SOX9-AS1):​n.32-17992C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,130 control chromosomes in the GnomAD database, including 35,091 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (35091 hom., cov: 33)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 16 publications found

Genes affected

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

ENSG00000288605 (HGNC:):

LINC02097 (HGNC:52948): (long intergenic non-protein coding RNA 2097)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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.32-17992C>G		intron	N/A
	SOX9-AS1	NR_103738.1		n.358+12186C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	ENST00000533232.5	TSL:1	n.32-17992C>G		intron	N/A
	SOX9-AS1	ENST00000414600.1	TSL:3	n.97-10916C>G		intron	N/A
	SOX9-AS1	ENST00000434703.5	TSL:2	n.358+12186C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102918 AN: 152008 Hom.: 35041 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.635

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.677 AC: 103028 AN: 152130 Hom.: 35091 Cov.: 33 AF XY: 0.681 AC XY: 50617 AN XY: 74372

African (AFR) AF: 0.716 AC: 29701 AN: 41508

American (AMR) AF: 0.702 AC: 10744 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.825 AC: 4270 AN: 5178

South Asian (SAS) AF: 0.630 AC: 3029 AN: 4810

European-Finnish (FIN) AF: 0.702 AC: 7420 AN: 10566

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44047 AN: 67982

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.656 Hom.: 3862

Bravo AF: 0.682

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.41
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs9913711; hg19: chr17-70098161;