Genetic Variant ASB18:c.206-121T>G (chr2-236241523-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_212556.4(ASB18):c.206-121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 1,163,224 control chromosomes in the GnomAD database, including 357,981 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 0.76 ( 44162 hom., cov: 32)

Exomes 𝑓: 0.79 ( 313819 hom. )

Consequence

ASB18
NM_212556.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980

Publications

9 publications found

Variant links:

Genes affected

ASB18 (HGNC:19770): (ankyrin repeat and SOCS box containing 18) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. They contain ankyrin repeat sequence and a 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, possibly targeting them for degradation. [provided by RefSeq, Feb 2017]

ASB18 links:

GBX2-AS1 (HGNC:55714): (GBX2 and ASB18 antisense RNA 1)

GBX2-AS1 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB18	NM_212556.4 link	c.206-121T>G		intron_variant	Intron 1 of 5	ENST00000409749.8	NP_997721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB18	ENST00000409749.8 link	c.206-121T>G		intron_variant	Intron 1 of 5	1	NM_212556.4	ENSP00000386532.3		Q6ZVZ8-1

Frequencies

GnomAD3 genomes

AF:

0.758

AC:

115208

AN:

151974

Hom.:

44132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.871

Gnomad AMR

AF:

0.805

Gnomad ASJ

AF:

0.842

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.819

Gnomad FIN

AF:

0.821

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.783

GnomAD2 exomes

AF:

0.801

AC:

127696

AN:

159386

AF XY:

0.803

show subpopulations

Gnomad AFR exome

AF:

0.653

Gnomad AMR exome

AF:

0.831

Gnomad ASJ exome

AF:

0.838

Gnomad EAS exome

AF:

0.793

Gnomad FIN exome

AF:

0.822

Gnomad NFE exome

AF:

0.795

Gnomad OTH exome

AF:

0.811

GnomAD4 exome

AF:

0.787

AC:

795496

AN:

1011132

Hom.:

313819

Cov.:

AF XY:

0.789

AC XY:

407419

AN XY:

516204

show subpopulations

African (AFR)

AF:

0.641

AC:

15767

AN:

24582

American (AMR)

AF:

0.825

AC:

29344

AN:

35570

Ashkenazi Jewish (ASJ)

AF:

0.841

AC:

19127

AN:

22752

East Asian (EAS)

AF:

0.839

AC:

29004

AN:

34562

South Asian (SAS)

AF:

0.819

AC:

59349

AN:

72424

European-Finnish (FIN)

AF:

0.821

AC:

35764

AN:

43582

Middle Eastern (MID)

AF:

0.804

AC:

3965

AN:

4930

European-Non Finnish (NFE)

AF:

0.781

AC:

567616

AN:

727224

Other (OTH)

AF:

0.781

AC:

35560

AN:

45506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

9477

18953

28430

37906

47383

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11196

22392

33588

44784

55980

<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:

0.758

AC:

115287

AN:

152092

Hom.:

44162

Cov.:

AF XY:

0.764

AC XY:

56785

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.652

AC:

27024

AN:

41466

American (AMR)

AF:

0.805

AC:

12303

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.842

AC:

2921

AN:

3470

East Asian (EAS)

AF:

0.797

AC:

4118

AN:

5168

South Asian (SAS)

AF:

0.820

AC:

3949

AN:

4818

European-Finnish (FIN)

AF:

0.821

AC:

8693

AN:

10586

Middle Eastern (MID)

AF:

0.830

AC:

244

AN:

294

European-Non Finnish (NFE)

AF:

0.788

AC:

53583

AN:

67986

Other (OTH)

AF:

0.786

AC:

1658

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1415

2830

4246

5661

7076

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

854

1708

2562

3416

4270

<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:

0.782

Hom.:

25677

Bravo

AF:

0.752

Asia WGS

AF:

0.811

AC:

2821

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.82

(source)

DANN

Benign

0.31

PhyloP100

-0.098

PromoterAI

0.020

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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