rs251456

Variant names:

• chr3-119025735-G-A
• rs251456
• NM_001015887.3:c.52+8796C>T

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+8796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,672 control chromosomes in the GnomAD database, including 1,262 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 0.12 (1262 hom., cov: 31)
• Consequence: IGSF11 NM_001015887.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF11	NM_001015887.3	c.52+8796C>T		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+8796C>T		intron_variant	Intron 1 of 6	1	NM_001015887.3	ENSP00000377370.2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18239 AN: 151554 Hom.: 1262 Cov.: 31

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.120 AC: 18244 AN: 151672 Hom.: 1262 Cov.: 31 AF XY: 0.122 AC XY: 9043 AN XY: 74118

African (AFR) AF: 0.0515 AC: 2133 AN: 41408

American (AMR) AF: 0.0983 AC: 1497 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3464

East Asian (EAS) AF: 0.205 AC: 1048 AN: 5118

South Asian (SAS) AF: 0.124 AC: 592 AN: 4792

European-Finnish (FIN) AF: 0.170 AC: 1785 AN: 10510

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10246 AN: 67848

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.135 Hom.: 314

Bravo AF: 0.111

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.40
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: rs251456; hg19: chr3-118744582;