16-83981071-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019065.3(NECAB2):āc.403G>Cā(p.Ala135Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_019065.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.403G>C | p.Ala135Pro | missense_variant | Exon 5 of 13 | ENST00000305202.9 | NP_061938.2 | |
NECAB2 | NM_001329748.1 | c.403G>C | p.Ala135Pro | missense_variant | Exon 5 of 12 | NP_001316677.1 | ||
NECAB2 | NM_001329749.2 | c.154G>C | p.Ala52Pro | missense_variant | Exon 4 of 12 | NP_001316678.1 | ||
NECAB2 | XM_047434240.1 | c.154G>C | p.Ala52Pro | missense_variant | Exon 4 of 12 | XP_047290196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.403G>C | p.Ala135Pro | missense_variant | Exon 5 of 13 | 1 | NM_019065.3 | ENSP00000307449.4 | ||
NECAB2 | ENST00000565691.5 | c.154G>C | p.Ala52Pro | missense_variant | Exon 3 of 11 | 1 | ENSP00000457354.1 | |||
NECAB2 | ENST00000566836.1 | c.76G>C | p.Ala26Pro | missense_variant | Exon 3 of 7 | 5 | ENSP00000455322.1 | |||
NECAB2 | ENST00000681513.1 | n.808G>C | non_coding_transcript_exon_variant | Exon 5 of 13 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135918
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.403G>C (p.A135P) alteration is located in exon 5 (coding exon 5) of the NECAB2 gene. This alteration results from a G to C substitution at nucleotide position 403, causing the alanine (A) at amino acid position 135 to be replaced by a proline (P). 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