17-72120683-G-GCA

Variant names:

• chr17-72120683-G-GCA
• rs1555628892
• ENST00000533232.5:n.31+79_31+80insTG

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+80insTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 151,030 control chromosomes in the GnomAD database, including 53 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.021 (53 hom., cov: 0)
  • Exomes 𝑓: 0.014 (0 hom.)
• Consequence: SOX9-AS1 ENST00000533232.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.511

Genes affected

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

ENSG00000288605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-72120683-G-GCA is Benign according to our data. Variant chr17-72120683-G-GCA is described in ClinVar as [Benign]. Clinvar id is 1229218.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0206 (3065/149110) while in subpopulation AFR AF= 0.0266 (1084/40740). AF 95% confidence interval is 0.0253. There are 53 homozygotes in gnomad4. There are 1635 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 53 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX9-AS1	NR_103737.1	n.31+78_31+79dupTG		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX9-AS1	ENST00000533232.5	n.31+79_31+80insTG		intron_variant	Intron 1 of 3	1
SOX9-AS1	ENST00000414600.1	n.96+21001_96+21002insTG		intron_variant	Intron 1 of 1	3
ENSG00000288605	ENST00000628742.2	n.147-35639_147-35638insTG		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3058 AN: 149018 Hom.: 52 Cov.: 0

Gnomad AFR AF: 0.0265

Gnomad AMI AF: 0.00785

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.00762

Gnomad SAS AF: 0.00471

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.0258

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0214

GnomAD4 exome AF: 0.0141 AC: 27 AN: 1920 Hom.: 0 AF XY: 0.0145 AC XY: 13 AN XY: 894

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0208

Gnomad4 ASJ exome AF: 0.0313

Gnomad4 EAS exome AF: 0.00847

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0148

Gnomad4 OTH exome AF: 0.0139

GnomAD4 genome AF: 0.0206 AC: 3065 AN: 149110 Hom.: 53 Cov.: 0 AF XY: 0.0225 AC XY: 1635 AN XY: 72582

Gnomad4 AFR AF: 0.0266

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.00784

Gnomad4 SAS AF: 0.00450

Gnomad4 FIN AF: 0.0617

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0212

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 08, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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: rs1555628892; hg19: chr17-70116824;