16-14857264-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014287.4(NOMO1):c.1011C>T(p.Asn337Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00865 in 150,012 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0086 ( 22 hom., cov: 29)
Exomes 𝑓: 0.00095 ( 24 hom. )
Failed GnomAD Quality Control
Consequence
NOMO1
NM_014287.4 synonymous
NM_014287.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.407
Genes affected
NOMO1 (HGNC:30060): (NODAL modulator 1) This gene encodes a protein originally thought to be related to the collagenase gene family. This gene is one of three highly similar genes in a region of duplication located on the p arm of chromosome 16. These three genes encode closely related proteins that may have the same function. The protein encoded by one of these genes has been identified as part of a protein complex that participates in the Nodal signaling pathway during vertebrate development. Mutations in ABCC6, which is located nearby, rather than mutations in this gene are associated with pseudoxanthoma elasticum (PXE). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 16-14857264-C-T is Benign according to our data. Variant chr16-14857264-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 710343.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.407 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00865 (1297/150012) while in subpopulation AFR AF= 0.0299 (1201/40128). AF 95% confidence interval is 0.0285. There are 22 homozygotes in gnomad4. There are 614 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 22 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOMO1 | ENST00000287667.12 | c.1011C>T | p.Asn337Asn | synonymous_variant | Exon 10 of 31 | 1 | NM_014287.4 | ENSP00000287667.7 | ||
NOMO1 | ENST00000566883.5 | n.303C>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 4 | |||||
NOMO1 | ENST00000566917.1 | n.487C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00863 AC: 1294AN: 149900Hom.: 22 Cov.: 29
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GnomAD3 exomes AF: 0.00275 AC: 376AN: 136728Hom.: 9 AF XY: 0.00214 AC XY: 155AN XY: 72292
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000952 AC: 1384AN: 1454126Hom.: 24 Cov.: 30 AF XY: 0.000865 AC XY: 626AN XY: 723780
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.00865 AC: 1297AN: 150012Hom.: 22 Cov.: 29 AF XY: 0.00838 AC XY: 614AN XY: 73290
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Feb 26, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at