16-66809460-A-G

Variant names:

• chr16-66809460-A-G
• rs363170
• NM_003905.4:c.1151-385T>C

Variant summary

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

The NM_003905.4(NAE1):​c.1151-385T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,282 control chromosomes in the GnomAD database, including 1,090 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 0.10 (1090 hom., cov: 32)
• Consequence: NAE1 NM_003905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 publications found

Genes affected

NAE1 (HGNC:621): (NEDD8 activating enzyme E1 subunit 1) The protein encoded by this gene binds to the beta-amyloid precursor protein. Beta-amyloid precursor protein is a cell surface protein with signal-transducing properties, and it is thought to play a role in the pathogenesis of Alzheimer's disease. In addition, the encoded protein can form a heterodimer with UBE1C and bind and activate NEDD8, a ubiquitin-like protein. This protein is required for cell cycle progression through the S/M checkpoint. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

NAE1 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia

  Inheritance: AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAE1	NM_003905.4	c.1151-385T>C		intron_variant	Intron 15 of 19	ENST00000290810.8	NP_003896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAE1	ENST00000290810.8	c.1151-385T>C		intron_variant	Intron 15 of 19	1	NM_003905.4	ENSP00000290810.3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15747 AN: 152164 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0842

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15744 AN: 152282 Hom.: 1090 Cov.: 32 AF XY: 0.0997 AC XY: 7423 AN XY: 74456

African (AFR) AF: 0.0273 AC: 1137 AN: 41586

American (AMR) AF: 0.0842 AC: 1286 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3472

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0930 AC: 449 AN: 4830

European-Finnish (FIN) AF: 0.115 AC: 1219 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10930 AN: 68006

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.135 Hom.: 1778

Bravo AF: 0.0974

Asia WGS AF: 0.0350 AC: 123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		1.0
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: rs363170; hg19: chr16-66843363;