chr7-106285885-C-A

Position:

• chr7-106285885-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609281.2(NAMPT-AS1):​n.686C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,160 control chromosomes in the GnomAD database, including 47,595 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 0.79 (47573 hom., cov: 31)
  • Exomes 𝑓: 0.75 (22 hom.)
• Consequence: NAMPT-AS1 ENST00000609281.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

Genes affected

NAMPT-AS1 (HGNC:56696): (NAMPT antisense RNA 1)

NAMPT (HGNC:30092): (nicotinamide phosphoribosyltransferase) This gene encodes a protein that catalyzes the condensation of nicotinamide with 5-phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, one step in the biosynthesis of nicotinamide adenine dinucleotide. The protein belongs to the nicotinic acid phosphoribosyltransferase (NAPRTase) family and is thought to be involved in many important biological processes, including metabolism, stress response and aging. This gene has a pseudogene on chromosome 10. [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAMPT	XM_047419699.1	c.-442G>T		5_prime_UTR_variant	1/12		XP_047275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAMPT-AS1	ENST00000609281.2	n.686C>A		non_coding_transcript_exon_variant	1/1
NAMPT	ENST00000424768.2	c.-442G>T		5_prime_UTR_variant	1/12	4		ENSP00000390591	P4
NAMPT	ENST00000681255.1	c.-392G>T		5_prime_UTR_variant	1/12			ENSP00000506129	P4

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119881 AN: 151966 Hom.: 47521 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.789

GnomAD4 exome AF: 0.750 AC: 57 AN: 76 Hom.: 22 Cov.: 0 AF XY: 0.795 AC XY: 35 AN XY: 44

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.789 AC: 119996 AN: 152084 Hom.: 47573 Cov.: 31 AF XY: 0.796 AC XY: 59186 AN XY: 74354

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.792

Alfa AF: 0.769 Hom.: 8371

Bravo AF: 0.789

Asia WGS AF: 0.944 AC: 3285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.8
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9770242; hg19: chr7-105926331;