Variant 17-72120678-T-TGCGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The ENST00000533232.5(SOX9-AS1):n.31+81_31+84dupGCGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00875 in 151,154 control chromosomes in the GnomAD database, including 6 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0089 ( 6 hom., cov: 31)

Exomes 𝑓: 0.0010 ( 0 hom. )

Consequence

SOX9-AS1
ENST00000533232.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.459

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 17-72120678-T-TGCGC is Benign according to our data. Variant chr17-72120678-T-TGCGC is described in ClinVar as [Likely_benign]. Clinvar id is 1196892.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00886 (1321/149146) while in subpopulation AFR AF= 0.0245 (997/40746). AF 95% confidence interval is 0.0232. There are 6 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOX9-AS1	NR_103737.1 linkuse as main transcript	n.31+81_31+84dupGCGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SOX9-AS1	ENST00000533232.5 linkuse as main transcript	n.31+81_31+84dupGCGC	intron_variant	1
SOX9-AS1	ENST00000414600.1 linkuse as main transcript	n.96+21003_96+21006dupGCGC	intron_variant	3
ENSG00000288605	ENST00000628742.2 linkuse as main transcript	n.147-35637_147-35634dupGCGC	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00876

AC:

1305

AN:

149042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00540

Gnomad ASJ

AF:

0.00849

Gnomad EAS

AF:

0.000602

Gnomad SAS

AF:

0.000212

Gnomad FIN

AF:

0.000390

Gnomad MID

AF:

0.00968

Gnomad NFE

AF:

0.00281

Gnomad OTH

AF:

0.00832

GnomAD4 exome

AF:

0.000996

AC:

AN:

2008

Hom.:

AF XY:

0.00105

AC XY:

AN XY:

952

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00179

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00886

AC:

1321

AN:

149146

Hom.:

Cov.:

AF XY:

0.00859

AC XY:

625

AN XY:

72762

show subpopulations

Gnomad4 AFR

AF:

0.0245

Gnomad4 AMR

AF:

0.00533

Gnomad4 ASJ

AF:

0.00849

Gnomad4 EAS

AF:

0.000603

Gnomad4 SAS

AF:

0.000212

Gnomad4 FIN

AF:

0.000390

Gnomad4 NFE

AF:

0.00281

Gnomad4 OTH

AF:

0.00823

Alfa

AF:

0.0000547

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2020

- -

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