chr13-34942962-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_001385012.1(NBEA):c.142G>A(p.Ala48Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,599,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001385012.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBEA | NM_001385012.1 | c.142G>A | p.Ala48Thr | missense_variant | 1/59 | ENST00000379939.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBEA | ENST00000379939.7 | c.142G>A | p.Ala48Thr | missense_variant | 1/59 | 5 | NM_001385012.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151664Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000129 AC: 3AN: 232802Hom.: 0 AF XY: 0.00000781 AC XY: 1AN XY: 128066
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448066Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 720022
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151664Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74066
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at