Genetic Variant ASB5:p.Gly93Asp (chr4-176222419-C-T) – ACMG Classification: Uncertain_significance (4 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_080874.4(ASB5):c.278G>A(p.Gly93Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000686 in 1,457,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G93S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

ASB5
NM_080874.4 missense, splice_region

Scores

Splicing: ADA: 0.9785

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.03

Variant links:

Genes affected

ASB5 (HGNC:17180): (ankyrin repeat and SOCS box containing 5) 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 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. Multiple alternatively spliced transcript variants have been described for this gene but their full length sequences are not known. [provided by RefSeq, Jul 2008]

ASB5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

MetaRNN computational evidence supports a deleterious effect, 0.885

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB5	NM_080874.4 link	c.278G>A	p.Gly93Asp	missense_variant, splice_region_variant	Exon 3 of 7	ENST00000296525.7	NP_543150.1	Q8WWX0-1Q5HYF3
ASB5	NM_001410863.1 link	c.143G>A	p.Gly48Asp	missense_variant, splice_region_variant	Exon 3 of 7		NP_001397792.1
ASB5	XM_005262759.2 link	c.278G>A	p.Gly93Asp	missense_variant, splice_region_variant	Exon 5 of 9		XP_005262816.1	Q8WWX0-1Q5HYF3
ASB5	XM_011531617.4 link	c.119G>A	p.Gly40Asp	missense_variant, splice_region_variant	Exon 3 of 7		XP_011529919.1	Q8WWX0-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ASB5	ENST00000296525.7 link	c.278G>A	p.Gly93Asp	missense_variant, splice_region_variant	Exon 3 of 7	1	NM_080874.4	ENSP00000296525.3	Q8WWX0-1
ASB5	ENST00000672074.1 link	c.143G>A	p.Gly48Asp	missense_variant, splice_region_variant	Exon 3 of 7			ENSP00000500617.1	A0A5F9ZHS2
ASB5	ENST00000512254.1 link	c.119G>A	p.Gly40Asp	missense_variant, splice_region_variant	Exon 3 of 7	2		ENSP00000422877.1	Q8WWX0-2
ASB5	ENST00000511879.1 link	n.363G>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.86e-7

AC:

AN:

1457900

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

725476

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.02e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.56

BayesDel_addAF

Pathogenic

0.32

BayesDel_noAF

Pathogenic

0.22

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.25

T;.

Eigen

Pathogenic

0.83

Eigen_PC

Pathogenic

0.80

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.97

D;D

M_CAP

Uncertain

0.10

MetaRNN

Pathogenic

0.89

D;D

MetaSVM

Uncertain

-0.18

MutationAssessor

Uncertain

2.6

M;.

PrimateAI

Pathogenic

0.83

PROVEAN

Pathogenic

-5.8

D;D

REVEL

Pathogenic

0.66

Sift

Uncertain

0.023

D;D

Sift4G

Uncertain

0.030

D;D

Polyphen

1.0

D;.

Vest4

0.88

MutPred

0.71

Loss of MoRF binding (P = 0.1057);.;

MVP

0.76

MPC

0.42

ClinPred

0.99

GERP RS

5.4

Varity_R

0.67

gMVP

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.98

dbscSNV1_RF

Pathogenic

0.73

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over