11-15253696-A-G

Variant names:

• chr11-15253696-A-G
• rs939046
• XM_017017698.2:c.1470+13173A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017017698.2(INSC):​c.1470+13173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,554 control chromosomes in the GnomAD database, including 7,411 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 0.29 (7411 hom., cov: 30)
• Consequence: INSC XM_017017698.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 4 publications found

Genes affected

INSC (HGNC:33116): (INSC spindle orientation adaptor protein) In Drosophila, neuroblasts divide asymmetrically into another neuroblast at the apical side and a smaller ganglion mother cell on the basal side. Cell polarization is precisely regulated by 2 apically localized multiprotein signaling complexes that are tethered by Inscuteable, which regulates their apical localization (Izaki et al., 2006 [PubMed 16458856]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43903 AN: 151438 Hom.: 7406 Cov.: 30

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.290 AC: 43923 AN: 151554 Hom.: 7411 Cov.: 30 AF XY: 0.299 AC XY: 22147 AN XY: 73956

African (AFR) AF: 0.146 AC: 6066 AN: 41408

American (AMR) AF: 0.356 AC: 5424 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3435 AN: 5110

South Asian (SAS) AF: 0.419 AC: 2006 AN: 4786

European-Finnish (FIN) AF: 0.390 AC: 4047 AN: 10376

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20823 AN: 67872

Other (OTH) AF: 0.328 AC: 686 AN: 2090

Alfa AF: 0.308 Hom.: 9580

Bravo AF: 0.283

Asia WGS AF: 0.513 AC: 1783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.1
DANN	Benign	0.61
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs939046; hg19: chr11-15275242;