rs10500885

Variant names:

• chr11-20993514-T-C
• rs10500885
• NM_006157.5:c.1300+32954T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-20993514-T-C
• chr11-20993514-T-G

Variant summary

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

The ENST00000357134.10(NELL1):​c.1300+32954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,042 control chromosomes in the GnomAD database, including 1,513 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 0.13 (1513 hom., cov: 31)
• Consequence: NELL1 ENST00000357134.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 2 publications found

Genes affected

NELL1 (HGNC:7750): (neural EGFL like 1) This gene encodes a cytoplasmic protein that contains epidermal growth factor (EGF)-like repeats. The encoded heterotrimeric protein may be involved in cell growth regulation and differentiation. A similar protein in rodents is involved in craniosynostosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357134.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NELL1	NM_006157.5	MANE Select	c.1300+32954T>C		intron	N/A	NP_006148.2
	NELL1	NM_001288713.1		c.1384+32954T>C		intron	N/A	NP_001275642.1
	NELL1	NM_201551.2		c.1300+32954T>C		intron	N/A	NP_963845.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NELL1	ENST00000357134.10	TSL:1 MANE Select	c.1300+32954T>C		intron	N/A	ENSP00000349654.5
	NELL1	ENST00000532434.5	TSL:1	c.1300+32954T>C		intron	N/A	ENSP00000437170.1
	NELL1	ENST00000298925.9	TSL:2	c.1384+32954T>C		intron	N/A	ENSP00000298925.5

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19802 AN: 151924 Hom.: 1511 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.130 AC: 19817 AN: 152042 Hom.: 1513 Cov.: 31 AF XY: 0.135 AC XY: 10016 AN XY: 74316

African (AFR) AF: 0.122 AC: 5056 AN: 41452

American (AMR) AF: 0.206 AC: 3142 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5168

South Asian (SAS) AF: 0.120 AC: 578 AN: 4804

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7735 AN: 67986

Other (OTH) AF: 0.117 AC: 246 AN: 2108

Alfa AF: 0.120 Hom.: 670

Bravo AF: 0.137

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		0.99
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: rs10500885; hg19: chr11-21015060;