Genetic Variant SOX9-AS1:n.31+79_31+80insTG (chr17-72120683-G-GCA) – 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+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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.511

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 17-72120683-G-GCA is Benign according to our data. Variant chr17-72120683-G-GCA is described in ClinVar as Benign. ClinVar VariationId 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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 53 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+78_31+79dupTG		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SOX9-AS1	ENST00000533232.5	TSL:1	n.31+79_31+80insTG	intron	N/A
SOX9-AS1	ENST00000414600.1	TSL:3	n.96+21001_96+21002insTG	intron	N/A
ENSG00000288605	ENST00000628742.2	TSL:5	n.147-35639_147-35638insTG	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0205

AC:

3058

AN:

149018

Hom.:

Cov.:

show subpopulations

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:

AN:

1920

Hom.:

AF XY:

0.0145

AC XY:

AN XY:

894

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0208

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0313

AC:

AN:

160

East Asian (EAS)

AF:

0.00847

AC:

AN:

354

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:

0.0148

AC:

AN:

1084

Other (OTH)

AF:

0.0139

AC:

AN:

144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

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:

0.0206

AC:

3065

AN:

149110

Hom.:

Cov.:

AF XY:

0.0225

AC XY:

1635

AN XY:

72582

show subpopulations

African (AFR)

AF:

0.0266

AC:

1084

AN:

40740

American (AMR)

AF:

0.0171

AC:

257

AN:

15026

Ashkenazi Jewish (ASJ)

AF:

0.0276

AC:

AN:

3442

East Asian (EAS)

AF:

0.00784

AC:

AN:

4972

South Asian (SAS)

AF:

0.00450

AC:

AN:

4662

European-Finnish (FIN)

AF:

0.0617

AC:

618

AN:

10012

Middle Eastern (MID)

AF:

0.0280

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0133

AC:

892

AN:

67004

Other (OTH)

AF:

0.0212

AC:

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

145

290

435

580

725

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.00675

Hom.:

ClinVar

ClinVar submissions

Significance: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

-0.51

Splicing

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

Publications

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17-72120683-GCACACACACA-GCACACACACACA

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