chr3-119027089-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0849 AC: 3528 AN: 41566

American (AMR) AF: 0.106 AC: 1615 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3472

East Asian (EAS) AF: 0.127 AC: 657 AN: 5184

South Asian (SAS) AF: 0.101 AC: 484 AN: 4810

European-Finnish (FIN) AF: 0.188 AC: 1993 AN: 10574

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10179 AN: 67978

Other (OTH) AF: 0.131 AC: 276 AN: 2108

Alfa AF: 0.136 Hom.: 2007

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
PhyloP100		-0.86
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: rs2160050; hg19: chr3-118745936;