rs5779167

Variant names:

• chr1-183312569-TAA-T
• rs5779167
• NM_015039.4:c.86-18778_86-18777delTT

Your query was ambiguous. Multiple possible variants found:

• chr1-183312569-TAA-T
• chr1-183312569-TAA-TA
• chr1-183312569-TAA-TAAA
• chr1-183312569-TAA-TAAAA
• chr1-183312569-TAA-TAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015039.4(NMNAT2):​c.86-18778_86-18777delTT 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 0.00034 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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.86-18778_86-18777delTT		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.86-18778_86-18777delTT		intron	N/A	ENSP00000287713.6	Q9BZQ4-1
	NMNAT2	ENST00000918147.1		c.86-18778_86-18777delTT		intron	N/A	ENSP00000588206.1
	ENSG00000305666	ENST00000812288.1		n.94+502_94+503delAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000336 AC: 50 AN: 148964 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000986

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000200

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00206

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000328

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000335 AC: 50 AN: 149058 Hom.: 0 Cov.: 0 AF XY: 0.000262 AC XY: 19 AN XY: 72580

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000983 AC: 4 AN: 40698

American (AMR) AF: 0.000200 AC: 3 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3436

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5138

South Asian (SAS) AF: 0.00 AC: 0 AN: 4706

European-Finnish (FIN) AF: 0.00206 AC: 20 AN: 9702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.000328 AC: 22 AN: 67100

Other (OTH) AF: 0.00 AC: 0 AN: 2052

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000000000156508), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 1081

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism

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: rs5779167; hg19: chr1-183281704;