chr16-83968768-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019065.3(NECAB2):c.120G>T(p.Glu40Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000127 in 948,426 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NECAB2 | NM_019065.3 | c.120G>T | p.Glu40Asp | missense_variant | 1/13 | ENST00000305202.9 | |
NECAB2 | NM_001329748.1 | c.120G>T | p.Glu40Asp | missense_variant | 1/12 | ||
NECAB2 | NM_001329749.2 | c.-104G>T | 5_prime_UTR_variant | 1/12 | |||
NECAB2 | XM_047434240.1 | c.-22-3383G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NECAB2 | ENST00000305202.9 | c.120G>T | p.Glu40Asp | missense_variant | 1/13 | 1 | NM_019065.3 | P1 | |
NECAB2 | ENST00000681513.1 | n.525G>T | non_coding_transcript_exon_variant | 1/13 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 0.0000127 AC: 12AN: 948426Hom.: 0 Cov.: 31 AF XY: 0.0000157 AC XY: 7AN XY: 445736
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.