rs1158699

chr3-118953229-C-T

Variant summary

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

The NM_001015887.3(IGSF11):c.53-22954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 151,982 control chromosomes in the GnomAD database, including 673 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 0.078 (673 hom., cov: 32)
• Consequence: IGSF11 NM_001015887.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

Genes affected

IGSF11 (HGNC:16669): (immunoglobulin superfamily member 11) IGSF11 is an immunoglobulin (Ig) superfamily member that is preferentially expressed in brain and testis. It shares significant homology with coxsackievirus and adenovirus receptor (CXADR; MIM 602621) and endothelial cell-selective adhesion molecule (ESAM).[supplied by OMIM, Apr 2005]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGSF11	NM_001015887.3	c.53-22954G>A		intron_variant		ENST00000393775.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGSF11	ENST00000393775.7	c.53-22954G>A		intron_variant		1	NM_001015887.3	P1

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11875 AN: 151862 Hom.: 671 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0783 AC: 11899 AN: 151982 Hom.: 673 Cov.: 32 AF XY: 0.0783 AC XY: 5815 AN XY: 74308

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0687 Hom.: 63

Bravo AF: 0.0909

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.8
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs1158699; hg19: chr3-118672076;