17-72120683-G-GCGCACA

Position:

• chr17-72120683-G-GCGCACA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000533232.5(SOX9-AS1):​n.31+79_31+80insTGTGCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00857 in 151,040 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0086 (15 hom., cov: 0)
  • Exomes 𝑓: 0.0036 (0 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.511

Genes affected

SOX9-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-72120683-G-GCGCACA is Benign according to our data. Variant chr17-72120683-G-GCGCACA is described in ClinVar as [Likely_benign]. Clinvar id is 1199135.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00364 (7/1922) while in subpopulation SAS AF= 0.111 (2/18). AF 95% confidence interval is 0.0197. There are 0 homozygotes in gnomad4_exome. There are 4 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX9-AS1	NR_103737.1	n.31+79_31+80insTGTGCG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOX9-AS1	ENST00000533232.5	n.31+79_31+80insTGTGCG		intron_variant		1
SOX9-AS1	ENST00000414600.1	n.96+21001_96+21002insTGTGCG		intron_variant		3
ENSG00000288605	ENST00000628742.2	n.147-35639_147-35638insTGTGCG		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00862 AC: 1285 AN: 149026 Hom.: 15 Cov.: 0

Gnomad AFR AF: 0.00642

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.00842

Gnomad EAS AF: 0.00561

Gnomad SAS AF: 0.00578

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00643

Gnomad OTH AF: 0.00975

GnomAD4 exome AF: 0.00364 AC: 7 AN: 1922 Hom.: 0 AF XY: 0.00447 AC XY: 4 AN XY: 894

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00843

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00864 AC: 1288 AN: 149118 Hom.: 15 Cov.: 0 AF XY: 0.00938 AC XY: 681 AN XY: 72588

Gnomad4 AFR AF: 0.00641

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.00842

Gnomad4 EAS AF: 0.00583

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.00643

Gnomad4 OTH AF: 0.00964

Alfa AF: 0.00587 Hom.: 349

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 19, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3837814; hg19: chr17-70116824;