rs4475916

Variant names:

• chr11-21367348-T-A
• rs4475916
• NM_006157.5:c.1550-3505T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-21367348-T-A
• chr11-21367348-T-C
• chr11-21367348-T-G

Variant summary

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

The NM_006157.5(NELL1):​c.1550-3505T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 151,812 control chromosomes in the GnomAD database, including 62,490 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 0.91 (62490 hom., cov: 29)
• Consequence: NELL1 NM_006157.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.908 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.1550-3505T>A		intron	N/A	NP_006148.2	Q92832-1
	NELL1	NM_001288713.1		c.1634-3505T>A		intron	N/A	NP_001275642.1	Q92832
	NELL1	NM_201551.2		c.1550-3505T>A		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.1550-3505T>A		intron	N/A	ENSP00000349654.5	Q92832-1
	NELL1	ENST00000532434.5	TSL:1	c.1550-3505T>A		intron	N/A	ENSP00000437170.1	Q92832-2
	NELL1	ENST00000534263.1	TSL:1	n.828-3505T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137529 AN: 151694 Hom.: 62440 Cov.: 29

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.907 AC: 137637 AN: 151812 Hom.: 62490 Cov.: 29 AF XY: 0.906 AC XY: 67208 AN XY: 74142

African (AFR) AF: 0.912 AC: 37775 AN: 41408

American (AMR) AF: 0.854 AC: 12986 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4687 AN: 5136

South Asian (SAS) AF: 0.878 AC: 4220 AN: 4806

European-Finnish (FIN) AF: 0.939 AC: 9869 AN: 10506

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62121 AN: 67968

Other (OTH) AF: 0.889 AC: 1872 AN: 2106

Alfa AF: 0.918 Hom.: 7965

Bravo AF: 0.899

Asia WGS AF: 0.882 AC: 3064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.53
PhyloP100		-0.25
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: rs4475916; hg19: chr11-21388894;