rs7220150

chr17-72212531-A-Cchr17-72212531-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532249.1(SOX9-AS1):n.73+8115T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,078 control chromosomes in the GnomAD database, including 2,880 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 0.19 (2880 hom., cov: 32)
• Consequence: SOX9-AS1 ENST00000532249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX9-AS1	ENST00000532249.1	n.73+8115T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28328 AN: 151960 Hom.: 2874 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28352 AN: 152078 Hom.: 2880 Cov.: 32 AF XY: 0.192 AC XY: 14312 AN XY: 74354

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.197

Alfa AF: 0.184 Hom.: 3481

Bravo AF: 0.185

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.2
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7220150; hg19: chr17-70208672;