rs1682859

Positions:

• chr11-133930324-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277285.4(IGSF9B):​c.1520-542G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,992 control chromosomes in the GnomAD database, including 33,683 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 0.66 (33683 hom., cov: 32)
• Consequence: IGSF9B NM_001277285.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGSF9B	NM_001277285.4	c.1520-542G>T		intron_variant		ENST00000533871.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGSF9B	ENST00000533871.8	c.1520-542G>T		intron_variant		5	NM_001277285.4	P1
IGSF9B	ENST00000321016.12	c.1520-542G>T		intron_variant		5
IGSF9B	ENST00000527648.2	n.1250-542G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100551 AN: 151874 Hom.: 33643 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.662 AC: 100652 AN: 151992 Hom.: 33683 Cov.: 32 AF XY: 0.658 AC XY: 48850 AN XY: 74280

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.665

Alfa AF: 0.673 Hom.: 33564

Bravo AF: 0.651

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs1682859; hg19: chr11-133800219;