3-118904752-AC-GT

Variant names:

• chr3-118904752-AC-GT
• NM_001015887.3:c.749_750delGTinsAC
• IGSF11 p.Gly250Asp

Variant summary

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

The NM_001015887.3(IGSF11):​c.749_750delGTinsAC​(p.Gly250Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IGSF11 NM_001015887.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.44
• 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.

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.749_750delGTinsAC	p.Gly250Asp	missense	N/A	NP_001015887.1	Q5DX21-1
	IGSF11	NM_001353318.2		c.899_900delGTinsAC	p.Gly300Asp	missense	N/A	NP_001340247.1
	IGSF11	NM_001353320.2		c.746_747delGTinsAC	p.Gly249Asp	missense	N/A	NP_001340249.1	Q5DX21-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF11	ENST00000393775.7	TSL:1 MANE Select	c.749_750delGTinsAC	p.Gly250Asp	missense	N/A	ENSP00000377370.2	Q5DX21-1
	IGSF11	ENST00000354673.6	TSL:1	c.746_747delGTinsAC	p.Gly249Asp	missense	N/A	ENSP00000346700.2	Q5DX21-2
	IGSF11	ENST00000874675.1		c.899_900delGTinsAC	p.Gly300Asp	missense	N/A	ENSP00000544734.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr3-118623599;