rs151344613

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting

The ENST00000420175.3(ASB10):​c.628C>T​(p.Arg210Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,608,814 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R210R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )

Consequence

ASB10
ENST00000420175.3 missense

Scores

1
8
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.59
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BS2
High AC in GnomAd4 at 6 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ASB10NM_001142459.2 linkuse as main transcriptc.628C>T p.Arg210Trp missense_variant 3/6 ENST00000420175.3 NP_001135931.2
ASB10NM_080871.4 linkuse as main transcriptc.583C>T p.Arg195Trp missense_variant 3/6 NP_543147.2
ASB10NM_001142460.1 linkuse as main transcriptc.628C>T p.Arg210Trp missense_variant 3/5 NP_001135932.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ASB10ENST00000420175.3 linkuse as main transcriptc.628C>T p.Arg210Trp missense_variant 3/61 NM_001142459.2 ENSP00000391137 P4Q8WXI3-1
ASB10ENST00000275838.5 linkuse as main transcriptc.628C>T p.Arg210Trp missense_variant 3/51 ENSP00000275838 Q8WXI3-2
ASB10ENST00000377867.7 linkuse as main transcriptc.583C>T p.Arg195Trp missense_variant 3/62 ENSP00000367098 A1Q8WXI3-3

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
6
AN:
152072
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000967
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:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000205
AC:
5
AN:
244464
Hom.:
0
AF XY:
0.0000225
AC XY:
3
AN XY:
133342
show subpopulations
Gnomad AFR exome
AF:
0.000129
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000164
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000227
AC:
33
AN:
1456742
Hom.:
0
Cov.:
34
AF XY:
0.0000207
AC XY:
15
AN XY:
723948
show subpopulations
Gnomad4 AFR exome
AF:
0.0000598
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000758
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000216
Gnomad4 OTH exome
AF:
0.0000499
GnomAD4 genome
AF:
0.0000395
AC:
6
AN:
152072
Hom.:
0
Cov.:
32
AF XY:
0.0000404
AC XY:
3
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.0000967
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:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000189
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000117
AC:
1
ExAC
AF:
0.0000247
AC:
3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
26
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.060
.;.;T
Eigen
Uncertain
0.43
Eigen_PC
Uncertain
0.27
FATHMM_MKL
Benign
0.37
N
LIST_S2
Uncertain
0.90
D;D;D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.46
T;T;T
MetaSVM
Uncertain
0.016
D
MutationAssessor
Uncertain
2.1
M;.;M
MutationTaster
Benign
0.81
D;D;D;D;D
PrimateAI
Benign
0.44
T
PROVEAN
Uncertain
-3.3
D;D;D
REVEL
Benign
0.22
Sift
Benign
0.037
D;D;D
Sift4G
Uncertain
0.059
T;T;T
Polyphen
1.0
.;D;D
Vest4
0.49
MVP
0.57
MPC
0.25
ClinPred
0.55
D
GERP RS
4.2
Varity_R
0.15
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
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

LitVar

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

Other links and lift over

dbSNP: rs151344613; hg19: chr7-150878502; COSMIC: COSV51997625; API