chr7-106285832-C-A

Position:

• chr7-106285832-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.633C>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 0.0947 in 152,516 control chromosomes in the GnomAD database, including 930 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 0.095 (926 hom., cov: 32)
  • Exomes 𝑓: 0.16 (4 hom.)
• Consequence: NAMPT-AS1 ENST00000609281.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542

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=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAMPT	XM_047419699.1	c.-389G>T		5_prime_UTR_variant	1/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAMPT-AS1	ENST00000609281.2	n.633C>A		non_coding_transcript_exon_variant	1/1
NAMPT	ENST00000424768.2	c.-389G>T		5_prime_UTR_variant	1/12	4		P4
NAMPT	ENST00000681255.1	c.-339G>T		5_prime_UTR_variant	1/12			P4

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14389 AN: 152024 Hom.: 926 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.155 AC: 58 AN: 374 Hom.: 4 Cov.: 0 AF XY: 0.172 AC XY: 34 AN XY: 198

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152142 Hom.: 926 Cov.: 32 AF XY: 0.0917 AC XY: 6820 AN XY: 74366

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0889 Hom.: 177

Bravo AF: 0.0918

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59744560; hg19: chr7-105926278;