16-83968768-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
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2024 | The c.120G>T (p.E40D) alteration is located in exon 1 (coding exon 1) of the NECAB2 gene. This alteration results from a G to T substitution at nucleotide position 120, causing the glutamic acid (E) at amino acid position 40 to be replaced by an aspartic acid (D). 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.