Variant 11-133921088-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001277285.4(IGSF9B):c.2637C>T(p.Phe879Phe) 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

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

IGSF9B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

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_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.078 with no splicing effect.

BA1

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	Protein	UniProt
IGSF9B	NM_001277285.4 linkuse as main transcript	c.2637C>T	p.Phe879Phe	synonymous_variant	18/20	ENST00000533871.8	NP_001264214.1	Q9UPX0-2Q8N7W7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGSF9B	ENST00000533871.8 linkuse as main transcript	c.2637C>T	p.Phe879Phe	synonymous_variant	18/20	5	NM_001277285.4	ENSP00000436552.2		Q9UPX0-2
IGSF9B	ENST00000321016.12 linkuse as main transcript	c.2637C>T	p.Phe879Phe	synonymous_variant	18/19	5		ENSP00000317980.8		Q9UPX0-1

Frequencies

GnomAD3 genomes

AF:

0.0220

AC:

3343

AN:

152234

Hom.:

101

Cov.:

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.:

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.:

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

AF:

0.0220

AC:

3351

AN:

152352

Hom.:

102

Cov.:

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.:

Bravo

AF:

0.0263

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.00322

EpiControl

AF:

0.00308

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over