chr2-100470489-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 8P and 10B. PVS1BP6_ModerateBA1
The NM_001011717.1(NMS):c.1A>G(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.00329 in 1,613,340 control chromosomes in the GnomAD database, including 197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0043 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 169 hom. )
Consequence
NMS
NM_001011717.1 start_lost
NM_001011717.1 start_lost
Scores
2
4
9
Clinical Significance
Conservation
PhyloP100: 4.21
Genes affected
NMS (HGNC:32203): (neuromedin S) This gene encodes a member of the neuromedin family of neuropeptides. The encoded preproprotein is proteolytically processed to generate a biologically active neuropeptide that plays a role in the regulation of circadian rhythm, anorexigenic action, antidiuretic action, cardiovascular function and stimulation of oxytocin and vasopressin release. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PVS1
?
Start lost variant, no new inframe start found.
BP6
?
Variant 2-100470489-A-G is Benign according to our data. Variant chr2-100470489-A-G is described in ClinVar as [Benign]. Clinvar id is 782803.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NMS | NM_001011717.1 | c.1A>G | p.Met1? | start_lost | 1/10 | ENST00000376865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMS | ENST00000376865.1 | c.1A>G | p.Met1? | start_lost | 1/10 | 1 | NM_001011717.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00434 AC: 660AN: 152134Hom.: 28 Cov.: 32
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?
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GnomAD3 exomes AF: 0.00840 AC: 2111AN: 251410Hom.: 92 AF XY: 0.00798 AC XY: 1084AN XY: 135876
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GnomAD4 exome AF: 0.00318 AC: 4641AN: 1461088Hom.: 169 Cov.: 30 AF XY: 0.00318 AC XY: 2313AN XY: 726926
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GnomAD4 genome ? AF: 0.00433 AC: 659AN: 152252Hom.: 28 Cov.: 32 AF XY: 0.00519 AC XY: 386AN XY: 74432
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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 | Aug 22, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
P
Vest4
MVP
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at