NM_018055.5:c.193+12C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018055.5(NODAL):c.193+12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 1,565,208 control chromosomes in the GnomAD database, including 152,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018055.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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NODAL | NM_018055.5 | c.193+12C>T | intron_variant | Intron 1 of 2 | ENST00000287139.8 | NP_060525.3 | ||
NODAL | NM_001329906.2 | c.-206-5480C>T | intron_variant | Intron 1 of 2 | NP_001316835.1 | |||
NODAL | XM_024448028.2 | c.-207+568C>T | intron_variant | Intron 1 of 2 | XP_024303796.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.357 AC: 54291AN: 152076Hom.: 11438 Cov.: 34
GnomAD3 exomes AF: 0.399 AC: 67551AN: 169238Hom.: 14503 AF XY: 0.396 AC XY: 36596AN XY: 92298
GnomAD4 exome AF: 0.440 AC: 621837AN: 1413016Hom.: 141077 Cov.: 42 AF XY: 0.436 AC XY: 304700AN XY: 699372
GnomAD4 genome AF: 0.357 AC: 54291AN: 152192Hom.: 11442 Cov.: 34 AF XY: 0.357 AC XY: 26548AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:5
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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Heterotaxy, visceral, 5, autosomal Benign:3
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:2
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Holoprosencephaly sequence Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at