17-72131395-T-C

Variant summary

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

The ENST00000414600.1(SOX9-AS1):n.96+10290A>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 0.488 in 151,964 control chromosomes in the GnomAD database, including 18,682 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 0.49 (18682 hom., cov: 32)
• Consequence: SOX9-AS1 ENST00000414600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

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 = 0.766 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	ENST00000414600.1	n.96+10290A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74076 AN: 151846 Hom.: 18651 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.488 AC: 74159 AN: 151964 Hom.: 18682 Cov.: 32 AF XY: 0.489 AC XY: 36304 AN XY: 74282

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.462

Alfa AF: 0.453 Hom.: 7725

Bravo AF: 0.504

Asia WGS AF: 0.567 AC: 1973 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	12
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9915657; hg19: chr17-70127536;