chr16-14844671-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_014287.4(NOMO1):c.302-3C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000082 ( 0 hom., cov: 13)
Exomes 𝑓: 0.00029 ( 4 hom. )
Failed GnomAD Quality Control
Consequence
NOMO1
NM_014287.4 splice_region, intron
NM_014287.4 splice_region, intron
Scores
2
Splicing: ADA: 0.0007105
2
Clinical Significance
Conservation
PhyloP100: 1.52
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 16-14844671-C-T is Benign according to our data. Variant chr16-14844671-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646241.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9AN: 109854Hom.: 0 Cov.: 13 FAILED QC
GnomAD3 genomes
AF:
AC:
9
AN:
109854
Hom.:
Cov.:
13
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000522 AC: 8AN: 15314Hom.: 0 AF XY: 0.000595 AC XY: 5AN XY: 8400
GnomAD3 exomes
AF:
AC:
8
AN:
15314
Hom.:
AF XY:
AC XY:
5
AN XY:
8400
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000295 AC: 140AN: 474836Hom.: 4 Cov.: 5 AF XY: 0.000426 AC XY: 105AN XY: 246718
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
140
AN:
474836
Hom.:
Cov.:
5
AF XY:
AC XY:
105
AN XY:
246718
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000819 AC: 9AN: 109912Hom.: 0 Cov.: 13 AF XY: 0.000119 AC XY: 6AN XY: 50330
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
9
AN:
109912
Hom.:
Cov.:
13
AF XY:
AC XY:
6
AN XY:
50330
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
NOMO1: BP4 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at