7-156950066-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_138400.2(NOM1):āc.329T>Cā(p.Leu110Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 1,391,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_138400.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOM1 | NM_138400.2 | c.329T>C | p.Leu110Pro | missense_variant | 1/11 | ENST00000275820.4 | NP_612409.1 | |
NOM1 | NM_001353366.2 | c.329T>C | p.Leu110Pro | missense_variant | 1/11 | NP_001340295.1 | ||
NOM1 | XR_927511.4 | n.355T>C | non_coding_transcript_exon_variant | 1/8 | ||||
NOM1 | XR_927513.4 | n.355T>C | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOM1 | ENST00000275820.4 | c.329T>C | p.Leu110Pro | missense_variant | 1/11 | 1 | NM_138400.2 | ENSP00000275820.3 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1391722Hom.: 0 Cov.: 33 AF XY: 0.00000146 AC XY: 1AN XY: 686860
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.