16-83990552-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_019065.3(NECAB2):c.518C>A(p.Thr173Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,884 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
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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>A | p.Thr173Lys | missense_variant | Exon 6 of 13 | ENST00000305202.9 | NP_061938.2 | |
NECAB2 | NM_001329748.1 | c.518C>A | p.Thr173Lys | missense_variant | Exon 6 of 12 | NP_001316677.1 | ||
NECAB2 | NM_001329749.2 | c.269C>A | p.Thr90Lys | missense_variant | Exon 5 of 12 | NP_001316678.1 | ||
NECAB2 | XM_047434240.1 | c.269C>A | p.Thr90Lys | 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>A | p.Thr173Lys | missense_variant | Exon 6 of 13 | 1 | NM_019065.3 | ENSP00000307449.4 | ||
NECAB2 | ENST00000565691.5 | c.269C>A | p.Thr90Lys | missense_variant | Exon 4 of 11 | 1 | ENSP00000457354.1 | |||
NECAB2 | ENST00000566836.1 | c.191C>A | p.Thr64Lys | missense_variant | Exon 4 of 7 | 5 | ENSP00000455322.1 | |||
NECAB2 | ENST00000681513.1 | n.923C>A | non_coding_transcript_exon_variant | Exon 6 of 13 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250512Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135458
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727242
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.518C>A (p.T173K) alteration is located in exon 6 (coding exon 6) of the NECAB2 gene. This alteration results from a C to A substitution at nucleotide position 518, causing the threonine (T) at amino acid position 173 to be replaced by a lysine (K). 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