chr11-133925324-T-C

Variant names:

• chr11-133925324-T-C
• rs329668
• NM_001277285.4:c.2034+415A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277285.4(IGSF9B):​c.2034+415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,186 control chromosomes in the GnomAD database, including 50,195 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (50195 hom., cov: 33)
• Consequence: IGSF9B NM_001277285.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF9B	NM_001277285.4	c.2034+415A>G		intron_variant	Intron 14 of 19	ENST00000533871.8	NP_001264214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGSF9B	ENST00000533871.8	c.2034+415A>G		intron_variant	Intron 14 of 19	5	NM_001277285.4	ENSP00000436552.2
IGSF9B	ENST00000321016.12	c.2034+415A>G		intron_variant	Intron 14 of 18	5		ENSP00000317980.8
IGSF9B	ENST00000527648.2	n.1764+415A>G		intron_variant	Intron 11 of 12	2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122985 AN: 152068 Hom.: 50165 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.831

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.809 AC: 123074 AN: 152186 Hom.: 50195 Cov.: 33 AF XY: 0.807 AC XY: 60057 AN XY: 74406

African (AFR) AF: 0.711 AC: 29496 AN: 41482

American (AMR) AF: 0.796 AC: 12188 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2993 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4472 AN: 5160

South Asian (SAS) AF: 0.767 AC: 3700 AN: 4826

European-Finnish (FIN) AF: 0.859 AC: 9107 AN: 10604

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58423 AN: 68018

Other (OTH) AF: 0.832 AC: 1760 AN: 2116

Alfa AF: 0.839 Hom.: 64518

Bravo AF: 0.797

Asia WGS AF: 0.818 AC: 2843 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs329668; hg19: chr11-133795219;