chr3-118902681-C-T

Variant names:

• chr3-118902681-C-T
• NM_001015887.3:c.1135G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001015887.3(IGSF11):​c.1135G>A​(p.Gly379Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: IGSF11 NM_001015887.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.14
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20843723).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001015887.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF11	NM_001015887.3	MANE Select	c.1135G>A	p.Gly379Arg	missense	Exon 7 of 7	NP_001015887.1	Q5DX21-1
	IGSF11	NM_001353318.2		c.1285G>A	p.Gly429Arg	missense	Exon 8 of 8	NP_001340247.1
	IGSF11	NM_001353319.2		c.1201G>A	p.Gly401Arg	missense	Exon 8 of 8	NP_001340248.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF11	ENST00000393775.7	TSL:1 MANE Select	c.1135G>A	p.Gly379Arg	missense	Exon 7 of 7	ENSP00000377370.2	Q5DX21-1
	IGSF11	ENST00000354673.6	TSL:1	c.1132G>A	p.Gly378Arg	missense	Exon 7 of 7	ENSP00000346700.2	Q5DX21-2
	IGSF11	ENST00000874675.1		c.1285G>A	p.Gly429Arg	missense	Exon 8 of 8	ENSP00000544734.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.019	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0075	T
Eigen	Benign	-0.020
Eigen_PC	Benign	0.11
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.85	D
M_CAP	Benign	0.064	D
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-0.32	T
MutationAssessor	Benign	1.1	L
PhyloP100		4.1
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.24
Sift	Uncertain	0.0030	D
Sift4G	Uncertain	0.0090	D
Polyphen		0.57	P
Vest4		0.15
MutPred		0.27		Gain of MoRF binding (P = 0.0241)
MVP		0.82
MPC		0.46
ClinPred		0.80	D
GERP RS		4.4
Varity_R		0.13
gMVP		0.57
Mutation Taster		=75/25	polymorphism

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

hg19: chr3-118621528;