Genetic Variant SOX9-AS1:n.31+84_31+85insGCGC (chr17-72120678-T-TGCGC) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The ENST00000533232.5(SOX9-AS1):n.31+84_31+85insGCGC 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

Publications

0 publications found

Variant links:

Genes affected

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

SOX9-AS1 links:

ENSG00000288605 (HGNC:):

ENSG00000288605 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533232.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX9-AS1	NR_103737.1		n.31+81_31+84dupGCGC		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SOX9-AS1	ENST00000533232.5	TSL:1	n.31+84_31+85insGCGC	intron	N/A
SOX9-AS1	ENST00000414600.1	TSL:3	n.96+21006_96+21007insGCGC	intron	N/A
ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35634_147-35633insGCGC	intron	N/A

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

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

178

East Asian (EAS)

AF:

0.00

AC:

AN:

378

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00179

AC:

AN:

1120

Other (OTH)

AF:

0.00

AC:

AN:

152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00886

AC:

1321

AN:

149146

Hom.:

Cov.:

AF XY:

0.00859

AC XY:

625

AN XY:

72762

show subpopulations

African (AFR)

AF:

0.0245

AC:

997

AN:

40746

American (AMR)

AF:

0.00533

AC:

AN:

14828

Ashkenazi Jewish (ASJ)

AF:

0.00849

AC:

AN:

3414

East Asian (EAS)

AF:

0.000603

AC:

AN:

4972

South Asian (SAS)

AF:

0.000212

AC:

AN:

4722

European-Finnish (FIN)

AF:

0.000390

AC:

AN:

10254

Middle Eastern (MID)

AF:

0.0104

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.00281

AC:

188

AN:

66970

Other (OTH)

AF:

0.00823

AC:

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

125

187

250

312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000547

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.46

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over