Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001142459.2(ASB10):c.-51_-50dupCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,483,822 control chromosomes in the GnomAD database, including 7,124 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 4939 hom., cov: 22)

Exomes 𝑓: 0.24 ( 2185 hom. )

Consequence

ASB10
NM_001142459.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.160

Publications

3 publications found

Variant links:

Genes affected

ASB10 (HGNC:17185): (ankyrin repeat and SOCS box containing 10) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. The SOCS box serves to couple suppressor of cytokine signaling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2008]

ASB10 Gene-Disease associations (from GenCC):

glaucoma 1, open angle, F
Inheritance: AD, Unknown Classification: LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

ASB10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 7-151187179-C-CAG is Benign according to our data. Variant chr7-151187179-C-CAG is described in ClinVar as Benign. ClinVar VariationId is 402398.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142459.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASB10	NM_001142459.2	MANE Select	c.-51_-50dupCT	5_prime_UTR	Exon 1 of 6	NP_001135931.2
ASB10	NM_001142460.1		c.-51_-50dupCT	5_prime_UTR	Exon 1 of 5	NP_001135932.2
ASB10	NM_080871.4		c.271+271_271+272dupCT	intron	N/A	NP_543147.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASB10	ENST00000420175.3	TSL:1 MANE Select	c.-51_-50dupCT	5_prime_UTR	Exon 1 of 6	ENSP00000391137.2
ASB10	ENST00000275838.5	TSL:1	c.-51_-50dupCT	5_prime_UTR	Exon 1 of 5	ENSP00000275838.1
ASB10	ENST00000377867.7	TSL:2	c.271+271_271+272dupCT	intron	N/A	ENSP00000367098.3

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

38552

AN:

150140

Hom.:

4933

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.359

Gnomad EAS

AF:

0.0807

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.279

GnomAD2 exomes

AF:

0.280

AC:

28084

AN:

100302

AF XY:

0.278

show subpopulations

Gnomad AFR exome

AF:

0.307

Gnomad AMR exome

AF:

0.265

Gnomad ASJ exome

AF:

0.341

Gnomad EAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.307

Gnomad OTH exome

AF:

0.302

GnomAD4 exome

AF:

0.238

AC:

317270

AN:

1333586

Hom.:

2185

Cov.:

AF XY:

0.236

AC XY:

155203

AN XY:

658378

show subpopulations

African (AFR)

AF:

0.220

AC:

6648

AN:

30218

American (AMR)

AF:

0.192

AC:

6654

AN:

34608

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

7082

AN:

24076

East Asian (EAS)

AF:

0.112

AC:

3878

AN:

34578

South Asian (SAS)

AF:

0.184

AC:

14104

AN:

76516

European-Finnish (FIN)

AF:

0.207

AC:

9770

AN:

47244

Middle Eastern (MID)

AF:

0.235

AC:

1296

AN:

5512

European-Non Finnish (NFE)

AF:

0.249

AC:

254906

AN:

1025192

Other (OTH)

AF:

0.232

AC:

12932

AN:

55642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

13968

27936

41903

55871

69839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9928

19856

29784

39712

49640

<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:

0.257

AC:

38583

AN:

150236

Hom.:

4939

Cov.:

AF XY:

0.251

AC XY:

18388

AN XY:

73366

show subpopulations

African (AFR)

AF:

0.247

AC:

10154

AN:

41062

American (AMR)

AF:

0.247

AC:

3728

AN:

15108

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

1239

AN:

3450

East Asian (EAS)

AF:

0.0813

AC:

414

AN:

5092

South Asian (SAS)

AF:

0.208

AC:

986

AN:

4748

European-Finnish (FIN)

AF:

0.225

AC:

2271

AN:

10088

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

18882

AN:

67400

Other (OTH)

AF:

0.280

AC:

583

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1429

2858

4286

5715

7144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.174

Hom.:

177

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=176/24

polymorphism (auto)

(source)

Splicing

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

Publications

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7-151187179-CAGAGAG-CAGAGAGAG

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

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over