chr3-118946108-C-G

Variant names:

• chr3-118946108-C-G
• rs10488303
• NM_001015887.3:c.53-15833G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001015887.3(IGSF11):​c.53-15833G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0247 in 151,964 control chromosomes in the GnomAD database, including 87 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 0.025 (87 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IGSF11 NM_001015887.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948
• Publications: 1 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]

IGSF11-AS1 (HGNC:40777): (IGSF11 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGSF11	NM_001015887.3	c.53-15833G>C		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.53-15833G>C		intron_variant	Intron 1 of 6	1	NM_001015887.3	ENSP00000377370.2

Frequencies

GnomAD3 genomes AF: 0.0247 AC: 3746 AN: 151846 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.00525

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0302

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0247 AC: 3752 AN: 151964 Hom.: 87 Cov.: 32 AF XY: 0.0255 AC XY: 1893 AN XY: 74268

African (AFR) AF: 0.00523 AC: 217 AN: 41470

American (AMR) AF: 0.0566 AC: 862 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 192 AN: 3470

East Asian (EAS) AF: 0.0654 AC: 337 AN: 5152

South Asian (SAS) AF: 0.0462 AC: 222 AN: 4800

European-Finnish (FIN) AF: 0.0112 AC: 118 AN: 10552

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1727 AN: 67968

Other (OTH) AF: 0.0304 AC: 64 AN: 2108

Alfa AF: 0.00767 Hom.: 1

Bravo AF: 0.0277

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		0.95
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10488303; hg19: chr3-118664955;