16-83990552-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_019065.3(NECAB2):c.518C>T(p.Thr173Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T173K) has been classified as Uncertain significance.
Frequency
Consequence
NM_019065.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.518C>T | p.Thr173Met | missense_variant | 6/13 | ENST00000305202.9 | |
NECAB2 | NM_001329748.1 | c.518C>T | p.Thr173Met | missense_variant | 6/12 | ||
NECAB2 | NM_001329749.2 | c.269C>T | p.Thr90Met | missense_variant | 5/12 | ||
NECAB2 | XM_047434240.1 | c.269C>T | p.Thr90Met | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.518C>T | p.Thr173Met | missense_variant | 6/13 | 1 | NM_019065.3 | P1 | |
NECAB2 | ENST00000565691.5 | c.269C>T | p.Thr90Met | missense_variant | 4/11 | 1 | |||
NECAB2 | ENST00000566836.1 | c.191C>T | p.Thr64Met | missense_variant | 4/7 | 5 | |||
NECAB2 | ENST00000681513.1 | n.923C>T | non_coding_transcript_exon_variant | 6/13 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250512Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135458
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727242
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.518C>T (p.T173M) alteration is located in exon 6 (coding exon 6) of the NECAB2 gene. This alteration results from a C to T substitution at nucleotide position 518, causing the threonine (T) at amino acid position 173 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at