Variant 17-72120683-G-GCGCA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000533232.5(SOX9-AS1):n.31+79_31+80insTGCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 150,846 control chromosomes in the GnomAD database, including 9,142 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 9127 hom., cov: 0)

Exomes 𝑓: 0.18 ( 15 hom. )

Consequence

SOX9-AS1
ENST00000533232.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.511

Variant links:

Genes affected

SOX9-AS1 (HGNC:):

SOX9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-72120683-G-GCGCA is Benign according to our data. Variant chr17-72120683-G-GCGCA is described in ClinVar as [Benign]. Clinvar id is 1264490.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SOX9-AS1	ENST00000533232.5 linkuse as main transcript	n.31+79_31+80insTGCG	intron_variant	1
SOX9-AS1	ENST00000414600.1 linkuse as main transcript	n.96+21001_96+21002insTGCG	intron_variant	3
ENSG00000288605	ENST00000628742.2 linkuse as main transcript	n.147-35639_147-35638insTGCG	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

47873

AN:

148858

Hom.:

9127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0989

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.499

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.214

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.320

GnomAD4 exome

AF:

0.180

AC:

342

AN:

1896

Hom.:

AF XY:

0.192

AC XY:

171

AN XY:

890

show subpopulations

Gnomad4 AFR exome

AF:

0.0714

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.234

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.321

AC:

47873

AN:

148950

Hom.:

9127

Cov.:

AF XY:

0.319

AC XY:

23138

AN XY:

72512

show subpopulations

Gnomad4 AFR

AF:

0.0986

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.498

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.428

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.149

Hom.:

349

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over