chr7-106277036-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005746.3(NAMPT):c.201T>C(p.Asn67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,585,116 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 40 hom. )
Consequence
NAMPT
NM_005746.3 synonymous
NM_005746.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.38
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 7-106277036-A-G is Benign according to our data. Variant chr7-106277036-A-G is described in ClinVar as [Benign]. Clinvar id is 707981.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.38 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0016 (244/152340) while in subpopulation EAS AF= 0.0451 (234/5190). AF 95% confidence interval is 0.0404. There are 9 homozygotes in gnomad4. There are 132 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 242 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAMPT | NM_005746.3 | c.201T>C | p.Asn67= | synonymous_variant | 2/11 | ENST00000222553.8 | |
NAMPT | XM_047419699.1 | c.201T>C | p.Asn67= | synonymous_variant | 3/12 | ||
NAMPT | XM_047419700.1 | c.201T>C | p.Asn67= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAMPT | ENST00000222553.8 | c.201T>C | p.Asn67= | synonymous_variant | 2/11 | 1 | NM_005746.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00159 AC: 242AN: 152222Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00369 AC: 926AN: 251150Hom.: 31 AF XY: 0.00353 AC XY: 480AN XY: 135796
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GnomAD4 exome AF: 0.00106 AC: 1514AN: 1432776Hom.: 40 Cov.: 28 AF XY: 0.00106 AC XY: 757AN XY: 714648
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at