1-183312569-TAA-TA

Position:

• chr1-183312569-TAA-TA

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NMNAT2	NM_015039.4	c.86-18777delT		intron_variant		ENST00000287713.7	NP_055854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NMNAT2	ENST00000287713.7	c.86-18777delT		intron_variant		1	NM_015039.4	ENSP00000287713.6

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

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.600

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs5779167; hg19: chr1-183281704;