Genetic Variant ENST00000609281.3:n.109C>G (chr7-106285307-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000609281.3(NAMPT-AS1):n.109C>G 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.704

Publications

28 publications found

Variant links:

Genes affected

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

NAMPT-AS1 links:

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]

NAMPT links:

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ACMG classification

Classification was made for transcript

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=-0.77).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
NAMPT-AS1	ENST00000609281.3 link	n.109C>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
NAMPT	ENST00000424768.2 link	c.-98+234G>C	intron_variant	Intron 1 of 11	4	ENSP00000390591.2	P43490C9JG65
NAMPT	ENST00000681255.1 link	c.-48+234G>C	intron_variant	Intron 1 of 11		ENSP00000506129.1	P43490

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

397234

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

187150

African (AFR)

AF:

0.00

AC:

AN:

7696

American (AMR)

AF:

0.00

AC:

AN:

880

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2976

East Asian (EAS)

AF:

0.00

AC:

AN:

2844

South Asian (SAS)

AF:

0.00

AC:

AN:

9372

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1344

Middle Eastern (MID)

AF:

0.00

AC:

AN:

810

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

357624

Other (OTH)

AF:

0.00

AC:

AN:

13688

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.1

(source)

DANN

Benign

0.35

PhyloP100

-0.70

PromoterAI

-0.052

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over