Variant 11-133921271-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001277285.4(IGSF9B):c.2454G>A(p.Ser818Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00619 in 1,611,166 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0064 ( 37 hom. )

Consequence

IGSF9B
NM_001277285.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.664

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 11-133921271-C-T is Benign according to our data. Variant chr11-133921271-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642551.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.664 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGSF9B	NM_001277285.4 linkuse as main transcript	c.2454G>A	p.Ser818Ser	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.2454G>A	p.Ser818Ser	synonymous_variant	18/20	5	NM_001277285.4	ENSP00000436552.2		Q9UPX0-2
IGSF9B	ENST00000321016.12 linkuse as main transcript	c.2454G>A	p.Ser818Ser	synonymous_variant	18/19	5		ENSP00000317980.8		Q9UPX0-1

Frequencies

GnomAD3 genomes

AF:

0.00468

AC:

713

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00366

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00923

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00726

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00422

AC:

1044

AN:

247416

Hom.:

AF XY:

0.00441

AC XY:

592

AN XY:

134356

show subpopulations

Gnomad AFR exome

AF:

0.00116

Gnomad AMR exome

AF:

0.00154

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.00863

Gnomad NFE exome

AF:

0.00658

Gnomad OTH exome

AF:

0.00382

GnomAD4 exome

AF:

0.00635

AC:

9268

AN:

1458828

Hom.:

Cov.:

AF XY:

0.00623

AC XY:

4523

AN XY:

725590

show subpopulations

Gnomad4 AFR exome

AF:

0.000867

Gnomad4 AMR exome

AF:

0.00177

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000986

Gnomad4 FIN exome

AF:

0.00804

Gnomad4 NFE exome

AF:

0.00755

Gnomad4 OTH exome

AF:

0.00408

GnomAD4 genome

AF:

0.00468

AC:

713

AN:

152338

Hom.:

Cov.:

AF XY:

0.00450

AC XY:

335

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00923

Gnomad4 NFE

AF:

0.00726

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00519

Hom.:

Bravo

AF:

0.00400

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00671

EpiControl

AF:

0.00848

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

IGSF9B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

2.3

DANN

Benign

0.84

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