Genetic Variant NM_080863.5:c.570-95C>G (chr17-44176643-C-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_080863.5(ASB16):c.570-95C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,578,052 control chromosomes in the GnomAD database, including 99,835 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.43 ( 15798 hom., cov: 32)

Exomes 𝑓: 0.33 ( 84037 hom. )

Consequence

ASB16
NM_080863.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.202

Publications

26 publications found

Variant links:

Genes affected

ASB16 (HGNC:19768): (ankyrin repeat and SOCS box containing 16) 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, Jul 2008]

ASB16 links:

ASB16-AS1 (HGNC:25442): (ASB16 antisense RNA 1)

ASB16-AS1 links:

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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 (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080863.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASB16	NM_080863.5	MANE Select	c.570-95C>G	intron	N/A	NP_543139.4
ASB16-AS1	NR_049729.1		n.1589G>C	non_coding_transcript_exon	Exon 4 of 4
ASB16-AS1	NR_049730.1		n.252-1G>C	splice_acceptor intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ASB16	ENST00000293414.6	TSL:1 MANE Select	c.570-95C>G	intron	N/A	ENSP00000293414.1	Q96NS5
ASB16	ENST00000589618.1	TSL:1	n.570-95C>G	intron	N/A	ENSP00000466033.1	K7ELE0
ASB16-AS1	ENST00000585457.6	TSL:2	n.1579G>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65079

AN:

151866

Hom.:

15758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.486

Gnomad EAS

AF:

0.773

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.303

Gnomad OTH

AF:

0.401

GnomAD2 exomes

AF:

0.389

AC:

96638

AN:

248656

AF XY:

0.371

show subpopulations

Gnomad AFR exome

AF:

0.643

Gnomad AMR exome

AF:

0.445

Gnomad ASJ exome

AF:

0.482

Gnomad EAS exome

AF:

0.785

Gnomad FIN exome

AF:

0.322

Gnomad NFE exome

AF:

0.302

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.329

AC:

468673

AN:

1426068

Hom.:

84037

Cov.:

AF XY:

0.326

AC XY:

231962

AN XY:

711504

show subpopulations

African (AFR)

AF:

0.643

AC:

21021

AN:

32670

American (AMR)

AF:

0.445

AC:

19855

AN:

44632

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

12431

AN:

25854

East Asian (EAS)

AF:

0.742

AC:

29278

AN:

39456

South Asian (SAS)

AF:

0.290

AC:

24592

AN:

84750

European-Finnish (FIN)

AF:

0.319

AC:

17039

AN:

53344

Middle Eastern (MID)

AF:

0.339

AC:

1934

AN:

5702

European-Non Finnish (NFE)

AF:

0.297

AC:

320392

AN:

1080496

Other (OTH)

AF:

0.374

AC:

22131

AN:

59164

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

14471

28941

43412

57882

72353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10780

21560

32340

43120

53900

<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:

0.429

AC:

65180

AN:

151984

Hom.:

15798

Cov.:

AF XY:

0.429

AC XY:

31897

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.634

AC:

26275

AN:

41452

American (AMR)

AF:

0.434

AC:

6622

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.486

AC:

1684

AN:

3466

East Asian (EAS)

AF:

0.773

AC:

3984

AN:

5154

South Asian (SAS)

AF:

0.306

AC:

1477

AN:

4824

European-Finnish (FIN)

AF:

0.315

AC:

3331

AN:

10576

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.303

AC:

20601

AN:

67942

Other (OTH)

AF:

0.401

AC:

845

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1770

3539

5309

7078

8848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.283

Hom.:

1094

Bravo

AF:

0.454

Asia WGS

AF:

0.521

AC:

1813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over