7-151176210-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001142459.2(ASB10):c.1306C>A(p.His436Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,609,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
ASB10
NM_001142459.2 missense
NM_001142459.2 missense
Scores
6
11
Clinical Significance
Conservation
PhyloP100: 2.85
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.12302396).
BP6
?
Variant 7-151176210-G-T is Benign according to our data. Variant chr7-151176210-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1661042.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASB10 | NM_001142459.2 | c.1306C>A | p.His436Asn | missense_variant | 5/6 | ENST00000420175.3 | |
ASB10 | NM_080871.4 | c.1261C>A | p.His421Asn | missense_variant | 5/6 | ||
ASB10 | NM_001142460.1 | c.1192C>A | p.His398Asn | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASB10 | ENST00000420175.3 | c.1306C>A | p.His436Asn | missense_variant | 5/6 | 1 | NM_001142459.2 | P4 | |
ASB10 | ENST00000275838.5 | c.1192C>A | p.His398Asn | missense_variant | 4/5 | 1 | |||
ASB10 | ENST00000377867.7 | c.1261C>A | p.His421Asn | missense_variant | 5/6 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000107 AC: 26AN: 243454Hom.: 0 AF XY: 0.0000828 AC XY: 11AN XY: 132852
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1457284Hom.: 0 Cov.: 31 AF XY: 0.0000152 AC XY: 11AN XY: 724896
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74484
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.1306C>A (p.H436N) alteration is located in exon 5 (coding exon 5) of the ASB10 gene. This alteration results from a C to A substitution at nucleotide position 1306, causing the histidine (H) at amino acid position 436 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 28, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;D;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.97
.;D;D
Vest4
MVP
MPC
0.25
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at