7-106285307-C-T

Position:

• chr7-106285307-C-T

Variant summary

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

The ENST00000609281.2(NAMPT-AS1):​n.108C>T 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 0.759 in 548,140 control chromosomes in the GnomAD database, including 158,965 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 0.77 (45168 hom., cov: 34)
  • Exomes 𝑓: 0.76 (113797 hom.)
• Consequence: NAMPT-AS1 ENST00000609281.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

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=-0.76).
• 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.-98+234G>A		intron_variant			XP_047275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAMPT-AS1	ENST00000609281.2	n.108C>T		non_coding_transcript_exon_variant	1/1
NAMPT	ENST00000424768.2	c.-98+234G>A		intron_variant		4		ENSP00000390591	P4
NAMPT	ENST00000681255.1	c.-48+234G>A		intron_variant				ENSP00000506129	P4
NAMPT	ENST00000681491.1	c.-98+11G>A		intron_variant				ENSP00000506540	P4

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116661 AN: 151988 Hom.: 45113 Cov.: 34

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.775

GnomAD4 exome AF: 0.755 AC: 299050 AN: 396034 Hom.: 113797 Cov.: 6 AF XY: 0.756 AC XY: 141061 AN XY: 186574

Gnomad4 AFR exome AF: 0.691

Gnomad4 AMR exome AF: 0.832

Gnomad4 ASJ exome AF: 0.763

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.870

Gnomad4 FIN exome AF: 0.820

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.783

GnomAD4 genome AF: 0.768 AC: 116777 AN: 152106 Hom.: 45168 Cov.: 34 AF XY: 0.776 AC XY: 57674 AN XY: 74368

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.778

Alfa AF: 0.763 Hom.: 19948

Bravo AF: 0.763

Asia WGS AF: 0.937 AC: 3261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.0
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319501; hg19: chr7-105925753;