dbSNP rs34383739: ASB10:c.-55_-50delCTCTCT (chr7-151187179-CAGAGAG-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001142459.2(ASB10):c.-55_-50delCTCTCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000808 in 1,497,150 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00045 ( 0 hom., cov: 22)

Exomes 𝑓: 0.000040 ( 0 hom. )

Consequence

ASB10
NM_001142459.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.639

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: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 67 AD,Unknown gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ASB10	NM_001142459.2 link	c.-55_-50delCTCTCT	5_prime_UTR_variant	Exon 1 of 6	ENST00000420175.3	NP_001135931.2	Q8WXI3-1
ASB10	NM_001142460.1 link	c.-55_-50delCTCTCT	5_prime_UTR_variant	Exon 1 of 5		NP_001135932.2	Q8WXI3-2A0A090N8I2
ASB10	NM_080871.4 link	c.271+267_271+272delCTCTCT	intron_variant	Intron 1 of 5		NP_543147.2	Q8WXI3-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ASB10	ENST00000420175.3 link	c.-55_-50delCTCTCT	5_prime_UTR_variant	Exon 1 of 6	1	NM_001142459.2	ENSP00000391137.2	Q8WXI3-1
ASB10	ENST00000275838.5 link	c.-55_-50delCTCTCT	5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000275838.1	Q8WXI3-2
ASB10	ENST00000377867.7 link	c.271+267_271+272delCTCTCT	intron_variant	Intron 1 of 5	2		ENSP00000367098.3	Q8WXI3-3
ASB10	ENST00000415615.1 link	n.121+69_121+74delCTCTCT	intron_variant	Intron 1 of 2	4		ENSP00000410871.1	F8WB38

Frequencies

GnomAD3 genomes

AF:

0.000446

AC:

AN:

150248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000397

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.00145

GnomAD2 exomes

AF:

0.0000399

AC:

AN:

100302

AF XY:

0.0000188

show subpopulations

Gnomad AFR exome

AF:

0.000541

Gnomad AMR exome

AF:

0.0000616

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000401

AC:

AN:

1346804

Hom.:

AF XY:

0.0000271

AC XY:

AN XY:

664724

show subpopulations

African (AFR)

AF:

0.00111

AC:

AN:

30560

American (AMR)

AF:

0.0000861

AC:

AN:

34842

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24256

East Asian (EAS)

AF:

0.00

AC:

AN:

34738

South Asian (SAS)

AF:

0.00

AC:

AN:

77052

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47470

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5536

European-Non Finnish (NFE)

AF:

0.0000135

AC:

AN:

1036226

Other (OTH)

AF:

0.0000535

AC:

AN:

56124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.000446

AC:

AN:

150346

Hom.:

Cov.:

AF XY:

0.000463

AC XY:

AN XY:

73416

show subpopulations

African (AFR)

AF:

0.00139

AC:

AN:

41096

American (AMR)

AF:

0.000397

AC:

AN:

15118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3450

East Asian (EAS)

AF:

0.00

AC:

AN:

5094

South Asian (SAS)

AF:

0.00

AC:

AN:

4756

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10114

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000148

AC:

AN:

67428

Other (OTH)

AF:

0.00144

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

177

Bravo

AF:

0.000400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.64

Splicing

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

Publications

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rs34383739

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over