Variant 17-72120683-GCA-G 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+78_31+79delTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 150,776 control chromosomes in the GnomAD database, including 52 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 52 hom., cov: 0)

Exomes 𝑓: 0.059 ( 0 hom. )

Consequence

SOX9-AS1
ENST00000533232.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.221

Variant links:

Genes affected

SOX9-AS1 (HGNC:):

SOX9-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-72120683-GCA-G is Benign according to our data. Variant chr17-72120683-GCA-G is described in ClinVar as [Benign]. Clinvar id is 1284079.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0752 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+78_31+79delTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SOX9-AS1	ENST00000533232.5 linkuse as main transcript	n.31+78_31+79delTG	intron_variant	1
SOX9-AS1	ENST00000414600.1 linkuse as main transcript	n.96+21000_96+21001delTG	intron_variant	3
ENSG00000288605	ENST00000628742.2 linkuse as main transcript	n.147-35640_147-35639delTG	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0147

AC:

2182

AN:

148840

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0495

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00586

Gnomad ASJ

AF:

0.000291

Gnomad EAS

AF:

0.000200

Gnomad SAS

AF:

0.00128

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0194

Gnomad NFE

AF:

0.000762

Gnomad OTH

AF:

0.00976

GnomAD4 exome

AF:

0.0590

AC:

109

AN:

1846

Hom.:

AF XY:

0.0621

AC XY:

AN XY:

854

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.0417

Gnomad4 ASJ exome

AF:

0.0909

Gnomad4 EAS exome

AF:

0.0298

Gnomad4 SAS exome

AF:

0.0556

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0611

Gnomad4 OTH exome

AF:

0.0435

GnomAD4 genome

AF:

0.0147

AC:

2186

AN:

148930

Hom.:

Cov.:

AF XY:

0.0143

AC XY:

1035

AN XY:

72480

show subpopulations

Gnomad4 AFR

AF:

0.0495

Gnomad4 AMR

AF:

0.00586

Gnomad4 ASJ

AF:

0.000291

Gnomad4 EAS

AF:

0.000201

Gnomad4 SAS

AF:

0.00129

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000762

Gnomad4 OTH

AF:

0.00965

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 23, 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