chr10-5652946-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024701.4(ASB13):​c.148G>A​(p.Val50Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000139 in 1,580,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. V50L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

ASB13
NM_024701.4 missense

Scores

8
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.27
Variant links:
Genes affected
ASB13 (HGNC:19765): (ankyrin repeat and SOCS box containing 13) 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. Multiple alternatively spliced transcript variants, both protein-coding and not protein-coding, have been described for this gene. [provided by RefSeq, Nov 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18247592).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ASB13NM_024701.4 linkc.148G>A p.Val50Met missense_variant Exon 2 of 6 ENST00000357700.11 NP_078977.2 Q8WXK3-1
ASB13NR_024581.2 linkn.192G>A non_coding_transcript_exon_variant Exon 2 of 5
ASB13NR_037164.2 linkn.192G>A non_coding_transcript_exon_variant Exon 2 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ASB13ENST00000357700.11 linkc.148G>A p.Val50Met missense_variant Exon 2 of 6 1 NM_024701.4 ENSP00000350331.6 Q8WXK3-1
ASB13ENST00000459912.5 linkn.148G>A non_coding_transcript_exon_variant Exon 2 of 7 1 ENSP00000433358.1 Q8WXK3-2
ASB13ENST00000479033.1 linkn.192G>A non_coding_transcript_exon_variant Exon 2 of 5 2

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152210
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000140
AC:
20
AN:
1427998
Hom.:
0
Cov.:
30
AF XY:
0.00000849
AC XY:
6
AN XY:
706846
show subpopulations
Gnomad4 AFR exome
AF:
0.0000606
Gnomad4 AMR exome
AF:
0.0000254
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000261
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000198
Gnomad4 NFE exome
AF:
0.0000137
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152210
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000277
Hom.:
0
Bravo
AF:
0.0000189
ESP6500AA
AF:
0.000228
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000252
AC:
3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.39
BayesDel_addAF
Benign
-0.032
T
BayesDel_noAF
Benign
-0.28
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.061
T
Eigen
Uncertain
0.20
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.90
D
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-1.6
N
REVEL
Benign
0.11
Sift
Uncertain
0.0090
D
Sift4G
Benign
0.23
T
Polyphen
0.056
B
Vest4
0.46
MVP
0.30
MPC
0.22
ClinPred
0.36
T
GERP RS
5.0
Varity_R
0.13
gMVP
0.35

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs375757990; hg19: chr10-5694909; COSMIC: COSV100731327; COSMIC: COSV100731327; API