rs1987307

Variant names:

• chr11-20952310-A-C
• rs1987307
• NM_006157.5:c.1171+4875A>C

Variant summary

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

The NM_006157.5(NELL1):​c.1171+4875A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,248 control chromosomes in the GnomAD database, including 417 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 0.064 (417 hom., cov: 32)
• Consequence: NELL1 NM_006157.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006157.5. 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
	NELL1	NM_006157.5	MANE Select	c.1171+4875A>C		intron	N/A	NP_006148.2	Q92832-1
	NELL1	NM_001288713.1		c.1255+4875A>C		intron	N/A	NP_001275642.1	Q92832
	NELL1	NM_201551.2		c.1171+4875A>C		intron	N/A	NP_963845.1	Q92832-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NELL1	ENST00000357134.10	TSL:1 MANE Select	c.1171+4875A>C		intron	N/A	ENSP00000349654.5	Q92832-1
	NELL1	ENST00000532434.5	TSL:1	c.1171+4875A>C		intron	N/A	ENSP00000437170.1	Q92832-2
	NELL1	ENST00000298925.9	TSL:2	c.1255+4875A>C		intron	N/A	ENSP00000298925.5	J3KNC5

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9726 AN: 152130 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0450

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0639 AC: 9722 AN: 152248 Hom.: 417 Cov.: 32 AF XY: 0.0631 AC XY: 4694 AN XY: 74428

African (AFR) AF: 0.0146 AC: 608 AN: 41550

American (AMR) AF: 0.0449 AC: 686 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.0847 AC: 438 AN: 5170

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4826

European-Finnish (FIN) AF: 0.0842 AC: 893 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6267 AN: 68018

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0823 Hom.: 336

Bravo AF: 0.0597

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	15
DANN	Benign	0.57
PhyloP100		1.1
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: rs1987307; hg19: chr11-20973856;