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GeneBe

11-133921088-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001277285.4(IGSF9B):c.2637C>T(p.Phe879=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00566 in 1,613,888 control chromosomes in the GnomAD database, including 212 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 102 hom., cov: 33)
Exomes 𝑓: 0.0040 ( 110 hom. )

Consequence

IGSF9B
NM_001277285.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0780
Variant links:
Genes affected
IGSF9B (HGNC:32326): (immunoglobulin superfamily member 9B) Predicted to enable kinase binding activity. Predicted to be involved in synaptic membrane adhesion. Predicted to act upstream of or within homophilic cell adhesion via plasma membrane adhesion molecules and positive regulation of inhibitory postsynaptic potential. Predicted to be located in dendrite; inhibitory synapse; and neuronal cell body. Predicted to be active in GABA-ergic synapse; neuron projection; and postsynaptic specialization of symmetric synapse. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 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=-0.53).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-133921088-G-A is Benign according to our data. Variant chr11-133921088-G-A is described in ClinVar as [Benign]. Clinvar id is 768500.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=0.078 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IGSF9BNM_001277285.4 linkuse as main transcriptc.2637C>T p.Phe879= synonymous_variant 18/20 ENST00000533871.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IGSF9BENST00000533871.8 linkuse as main transcriptc.2637C>T p.Phe879= synonymous_variant 18/205 NM_001277285.4 P1Q9UPX0-2
IGSF9BENST00000321016.12 linkuse as main transcriptc.2637C>T p.Phe879= synonymous_variant 18/195 Q9UPX0-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0220
AC:
3343
AN:
152234
Hom.:
101
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0672
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0195
Gnomad ASJ
AF:
0.0112
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.00220
Gnomad OTH
AF:
0.0287
GnomAD3 exomes
AF:
0.00752
AC:
1872
AN:
249072
Hom.:
43
AF XY:
0.00606
AC XY:
819
AN XY:
135132
show subpopulations
Gnomad AFR exome
AF:
0.0693
Gnomad AMR exome
AF:
0.0107
Gnomad ASJ exome
AF:
0.0115
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00229
Gnomad OTH exome
AF:
0.00826
GnomAD4 exome
AF:
0.00396
AC:
5787
AN:
1461536
Hom.:
110
Cov.:
34
AF XY:
0.00361
AC XY:
2624
AN XY:
727052
show subpopulations
Gnomad4 AFR exome
AF:
0.0683
Gnomad4 AMR exome
AF:
0.0113
Gnomad4 ASJ exome
AF:
0.0120
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000220
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.00173
Gnomad4 OTH exome
AF:
0.0105
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0220
AC:
3351
AN:
152352
Hom.:
102
Cov.:
33
AF XY:
0.0211
AC XY:
1572
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.0672
Gnomad4 AMR
AF:
0.0195
Gnomad4 ASJ
AF:
0.0112
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00220
Gnomad4 OTH
AF:
0.0284
Alfa
AF:
0.0118
Hom.:
27
Bravo
AF:
0.0263
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.00322
EpiControl
AF:
0.00308

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 13, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
Cadd
Benign
3.4
Dann
Benign
0.82

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: rs77730320; hg19: chr11-133790983; API