rs2160050

Variant names:

• chr3-119027089-T-C
• rs2160050
• NM_001015887.3:c.52+7442A>G

Variant summary

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

The NM_001015887.3(IGSF11):​c.52+7442A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,182 control chromosomes in the GnomAD database, including 1,373 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 0.13 (1373 hom., cov: 32)
• Consequence: IGSF11 NM_001015887.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF11	NM_001015887.3	c.52+7442A>G		intron_variant	Intron 1 of 6	ENST00000393775.7	NP_001015887.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGSF11	ENST00000393775.7	c.52+7442A>G		intron_variant	Intron 1 of 6	1	NM_001015887.3	ENSP00000377370.2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19460 AN: 152064 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.128 AC: 19477 AN: 152182 Hom.: 1373 Cov.: 32 AF XY: 0.129 AC XY: 9574 AN XY: 74380

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.131

Alfa AF: 0.149 Hom.: 237

Bravo AF: 0.120

Asia WGS AF: 0.103 AC: 355 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
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: rs2160050; hg19: chr3-118745936;