chr17-72102020-G-C

Position:

• chr17-72102020-G-C

Variant summary

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

The NR_103738.1(SOX9-AS1):​n.358+12186C>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 0.677 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 NR_103738.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOX9-AS1	NR_103738.1	n.358+12186C>G		intron_variant, non_coding_transcript_variant
SOX9-AS1	NR_103737.1	n.32-17992C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX9-AS1	ENST00000662263.1	n.44-16975C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.636

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9913711; hg19: chr17-70098161;