chr3-118957645-T-C

Variant names:

• chr3-118957645-T-C
• rs4687833
• NM_001015887.3:c.53-27370A>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.53-27370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,192 control chromosomes in the GnomAD database, including 50,801 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 0.82 (50801 hom., cov: 32)
• Consequence: IGSF11 NM_001015887.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

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.53-27370A>G		intron	N/A	NP_001015887.1	Q5DX21-1
	IGSF11	NM_001353318.2		c.202+24146A>G		intron	N/A	NP_001340247.1
	IGSF11	NM_001353319.2		c.202+24146A>G		intron	N/A	NP_001340248.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGSF11	ENST00000393775.7	TSL:1 MANE Select	c.53-27370A>G		intron	N/A	ENSP00000377370.2	Q5DX21-1
	IGSF11	ENST00000354673.6	TSL:1	c.50-27370A>G		intron	N/A	ENSP00000346700.2	Q5DX21-2
	IGSF11	ENST00000874675.1		c.202+24146A>G		intron	N/A	ENSP00000544734.1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124093 AN: 152074 Hom.: 50753 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.816 AC: 124206 AN: 152192 Hom.: 50801 Cov.: 32 AF XY: 0.816 AC XY: 60742 AN XY: 74402

African (AFR) AF: 0.857 AC: 35597 AN: 41514

American (AMR) AF: 0.813 AC: 12434 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3470

East Asian (EAS) AF: 0.801 AC: 4147 AN: 5180

South Asian (SAS) AF: 0.850 AC: 4100 AN: 4826

European-Finnish (FIN) AF: 0.815 AC: 8618 AN: 10576

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54143 AN: 68010

Other (OTH) AF: 0.796 AC: 1682 AN: 2114

Alfa AF: 0.800 Hom.: 91022

Bravo AF: 0.820

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.70
PhyloP100		-0.27
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: rs4687833; hg19: chr3-118676492;