rs1319501

Variant names:

• chr7-106285307-C-A
• rs1319501
• ENST00000609281.3:n.109C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-106285307-C-A
• chr7-106285307-C-G
• chr7-106285307-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000609281.3(NAMPT-AS1):​n.109C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NAMPT-AS1 ENST00000609281.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 28 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAMPT-AS1	NR_186647.1	n.62C>A		non_coding_transcript_exon_variant	Exon 1 of 1
NAMPT	XM_047419699.1	c.-98+234G>T		intron_variant	Intron 1 of 11		XP_047275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAMPT-AS1	ENST00000609281.3	n.109C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
NAMPT	ENST00000424768.2	c.-98+234G>T		intron_variant	Intron 1 of 11	4		ENSP00000390591.2
NAMPT	ENST00000681255.1	c.-48+234G>T		intron_variant	Intron 1 of 11			ENSP00000506129.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 397234 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 187150

African (AFR) AF: 0.00 AC: 0 AN: 7696

American (AMR) AF: 0.00 AC: 0 AN: 880

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2976

East Asian (EAS) AF: 0.00 AC: 0 AN: 2844

South Asian (SAS) AF: 0.00 AC: 0 AN: 9372

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1344

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 810

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 357624

Other (OTH) AF: 0.00 AC: 0 AN: 13688

GnomAD4 genome Cov.: 34

Alfa AF: 0.0000106 Hom.: 27533

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.70
PromoterAI		-0.040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1319501; hg19: chr7-105925753;