1-183312569-TAA-TA

Variant names:

• chr1-183312569-TA-T
• rs5779167
• NM_015039.4:c.86-18777delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015039.4(NMNAT2):​c.86-18777delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (24666 hom., cov: 0)
• Consequence: NMNAT2 NM_015039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 0 publications found

Genes affected

NMNAT2 (HGNC:16789): (nicotinamide nucleotide adenylyltransferase 2) This gene product belongs to the nicotinamide mononucleotide adenylyltransferase (NMNAT) enzyme family, members of which catalyze an essential step in NAD (NADP) biosynthetic pathway. Unlike the other human family member, which is localized to the nucleus, and is ubiquitously expressed; this enzyme is cytoplasmic, and is predominantly expressed in the brain. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000305666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015039.4. 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
	NMNAT2	NM_015039.4	MANE Select	c.86-18777delT		intron	N/A	NP_055854.1	Q9BZQ4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMNAT2	ENST00000287713.7	TSL:1 MANE Select	c.86-18777delT		intron	N/A	ENSP00000287713.6	Q9BZQ4-1
	NMNAT2	ENST00000918147.1		c.86-18777delT		intron	N/A	ENSP00000588206.1
	ENSG00000305666	ENST00000812288.1		n.94+502delA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.574 AC: 85535 AN: 148976 Hom.: 24659 Cov.: 0

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.600

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.574 AC: 85555 AN: 149070 Hom.: 24666 Cov.: 0 AF XY: 0.580 AC XY: 42078 AN XY: 72584

African (AFR) AF: 0.475 AC: 19342 AN: 40684

American (AMR) AF: 0.576 AC: 8657 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2251 AN: 3438

East Asian (EAS) AF: 0.801 AC: 4121 AN: 5144

South Asian (SAS) AF: 0.621 AC: 2922 AN: 4702

European-Finnish (FIN) AF: 0.691 AC: 6716 AN: 9720

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.590 AC: 39598 AN: 67098

Other (OTH) AF: 0.600 AC: 1231 AN: 2050

Alfa AF: 0.422 Hom.: 1081

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.41
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5779167;

hg19: chr1-183281704;