Genetic Variant ASB1:c.*409A>G (chr2-238446920-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040445.3(ASB1):c.*409A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 180,514 control chromosomes in the GnomAD database, including 3,823 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 3734 hom., cov: 32)

Exomes 𝑓: 0.056 ( 89 hom. )

Consequence

ASB1
NM_001040445.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.708

Publications

5 publications found

Variant links:

Genes affected

ASB1 (HGNC:16011): (ankyrin repeat and SOCS box containing 1) The protein encoded by this gene contains an ankyrin repeat sequence and SOCS box domain. The SOCS box serves to couple suppressor of cytokine signalling (SOCS) proteins and their binding partners with the elongin B and C complex, targeting them for ubiquitination and degradation. [provided by RefSeq, Aug 2016]

ASB1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB1	NM_001040445.3 link	c.*409A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000264607.9	NP_001035535.1	Q9Y576
ASB1	NM_001330196.2 link	c.*409A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001317125.1	B9A047

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB1	ENST00000264607.9 link	c.*409A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_001040445.3	ENSP00000264607.4		Q9Y576
ASB1	ENST00000481566.1 link	n.272+265A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24129

AN:

151992

Hom.:

3720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.398

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0415

Gnomad OTH

AF:

0.137

GnomAD4 exome

AF:

0.0564

AC:

1601

AN:

28404

Hom.:

Cov.:

AF XY:

0.0562

AC XY:

843

AN XY:

14996

show subpopulations

African (AFR)

AF:

0.394

AC:

AN:

208

American (AMR)

AF:

0.0858

AC:

266

AN:

3100

Ashkenazi Jewish (ASJ)

AF:

0.0243

AC:

AN:

536

East Asian (EAS)

AF:

0.113

AC:

AN:

542

South Asian (SAS)

AF:

0.0903

AC:

393

AN:

4352

European-Finnish (FIN)

AF:

0.0740

AC:

AN:

838

Middle Eastern (MID)

AF:

0.0769

AC:

AN:

104

European-Non Finnish (NFE)

AF:

0.0353

AC:

611

AN:

17292

Other (OTH)

AF:

0.0733

AC:

105

AN:

1432

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

139

209

278

348

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.159

AC:

24184

AN:

152110

Hom.:

3734

Cov.:

AF XY:

0.161

AC XY:

11938

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.398

AC:

16497

AN:

41422

American (AMR)

AF:

0.124

AC:

1896

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

137

AN:

3470

East Asian (EAS)

AF:

0.139

AC:

722

AN:

5178

South Asian (SAS)

AF:

0.117

AC:

562

AN:

4820

European-Finnish (FIN)

AF:

0.114

AC:

1210

AN:

10594

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0415

AC:

2820

AN:

68014

Other (OTH)

AF:

0.136

AC:

287

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

836

1671

2507

3342

4178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<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:

0.0978

Hom.:

3267

Bravo

AF:

0.169

Asia WGS

AF:

0.124

AC:

429

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

(source)

DANN

Benign

0.52

PhyloP100

-0.71

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over