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rs61734407

Positions:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001142459.2(ASB10):​c.1024C>T​(p.Leu342=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,606,700 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0054 ( 62 hom. )

Consequence

ASB10
NM_001142459.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 0.341
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 Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-151181019-G-A is Benign according to our data. Variant chr7-151181019-G-A is described in ClinVar as [Benign]. Clinvar id is 99990.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.341 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd4 at 603 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASB10NM_001142459.2 linkuse as main transcriptc.1024C>T p.Leu342= synonymous_variant 3/6 ENST00000420175.3
ASB10NM_080871.4 linkuse as main transcriptc.979C>T p.Leu327= synonymous_variant 3/6
ASB10NM_001142460.1 linkuse as main transcriptc.1024C>T p.Leu342= synonymous_variant 3/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASB10ENST00000420175.3 linkuse as main transcriptc.1024C>T p.Leu342= synonymous_variant 3/61 NM_001142459.2 P4Q8WXI3-1
ASB10ENST00000275838.5 linkuse as main transcriptc.1024C>T p.Leu342= synonymous_variant 3/51 Q8WXI3-2
ASB10ENST00000377867.7 linkuse as main transcriptc.979C>T p.Leu327= synonymous_variant 3/62 A1Q8WXI3-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00397
AC:
604
AN:
152244
Hom.:
6
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00116
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00320
Gnomad ASJ
AF:
0.0467
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.000470
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00451
Gnomad OTH
AF:
0.0115
GnomAD3 exomes
AF:
0.00510
AC:
1240
AN:
243130
Hom.:
13
AF XY:
0.00525
AC XY:
698
AN XY:
132902
show subpopulations
Gnomad AFR exome
AF:
0.000580
Gnomad AMR exome
AF:
0.00302
Gnomad ASJ exome
AF:
0.0460
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00239
Gnomad FIN exome
AF:
0.000529
Gnomad NFE exome
AF:
0.00507
Gnomad OTH exome
AF:
0.00716
GnomAD4 exome
AF:
0.00538
AC:
7818
AN:
1454338
Hom.:
62
Cov.:
31
AF XY:
0.00538
AC XY:
3889
AN XY:
722258
show subpopulations
Gnomad4 AFR exome
AF:
0.00123
Gnomad4 AMR exome
AF:
0.00346
Gnomad4 ASJ exome
AF:
0.0484
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00244
Gnomad4 FIN exome
AF:
0.000698
Gnomad4 NFE exome
AF:
0.00503
Gnomad4 OTH exome
AF:
0.00748
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00396
AC:
603
AN:
152362
Hom.:
6
Cov.:
33
AF XY:
0.00382
AC XY:
285
AN XY:
74516
show subpopulations
Gnomad4 AFR
AF:
0.00115
Gnomad4 AMR
AF:
0.00320
Gnomad4 ASJ
AF:
0.0467
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.000470
Gnomad4 NFE
AF:
0.00451
Gnomad4 OTH
AF:
0.0114
Alfa
AF:
0.00769
Hom.:
8
Bravo
AF:
0.00467
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.00611
EpiControl
AF:
0.00557

ClinVar

Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 06, 2023- -
Glaucoma 1, open angle, F Other:1
not provided, no classification providedliterature onlyCasey Eye Institute Glaucoma Genetics Lab -- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
5.2
DANN
Benign
0.68

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: rs61734407; hg19: chr7-150878106; API