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 (★).
Frequency
Consequence
NM_019065.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.518C>T | p.Thr173Met | missense_variant | Exon 6 of 13 | ENST00000305202.9 | NP_061938.2 | |
NECAB2 | NM_001329748.1 | c.518C>T | p.Thr173Met | missense_variant | Exon 6 of 12 | NP_001316677.1 | ||
NECAB2 | NM_001329749.2 | c.269C>T | p.Thr90Met | missense_variant | Exon 5 of 12 | NP_001316678.1 | ||
NECAB2 | XM_047434240.1 | c.269C>T | p.Thr90Met | missense_variant | Exon 5 of 12 | XP_047290196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.518C>T | p.Thr173Met | missense_variant | Exon 6 of 13 | 1 | NM_019065.3 | ENSP00000307449.4 | ||
NECAB2 | ENST00000565691.5 | c.269C>T | p.Thr90Met | missense_variant | Exon 4 of 11 | 1 | ENSP00000457354.1 | |||
NECAB2 | ENST00000566836.1 | c.191C>T | p.Thr64Met | missense_variant | Exon 4 of 7 | 5 | ENSP00000455322.1 | |||
NECAB2 | ENST00000681513.1 | n.923C>T | non_coding_transcript_exon_variant | Exon 6 of 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
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