16-83968832-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019065.3(NECAB2):āc.184A>Cā(p.Thr62Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000084 in 952,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.184A>C | p.Thr62Pro | missense_variant | 1/13 | ENST00000305202.9 | |
NECAB2 | NM_001329748.1 | c.184A>C | p.Thr62Pro | missense_variant | 1/12 | ||
NECAB2 | NM_001329749.2 | c.-40A>C | 5_prime_UTR_variant | 1/12 | |||
NECAB2 | XM_047434240.1 | c.-22-3319A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.184A>C | p.Thr62Pro | missense_variant | 1/13 | 1 | NM_019065.3 | P1 | |
NECAB2 | ENST00000681513.1 | n.589A>C | non_coding_transcript_exon_variant | 1/13 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 0.00000840 AC: 8AN: 952882Hom.: 0 Cov.: 30 AF XY: 0.00000894 AC XY: 4AN XY: 447226
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.184A>C (p.T62P) alteration is located in exon 1 (coding exon 1) of the NECAB2 gene. This alteration results from a A to C substitution at nucleotide position 184, causing the threonine (T) at amino acid position 62 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
Publications
No publications associated with this variant yet.