2-15167080-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015909.4(NBAS):āc.7084A>Gā(p.Thr2362Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,608,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. T2362T) has been classified as Likely benign.
Frequency
Consequence
NM_015909.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBAS | NM_015909.4 | c.7084A>G | p.Thr2362Ala | missense_variant | 52/52 | ENST00000281513.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBAS | ENST00000281513.10 | c.7084A>G | p.Thr2362Ala | missense_variant | 52/52 | 1 | NM_015909.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247716Hom.: 0 AF XY: 0.00000747 AC XY: 1AN XY: 133806
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456764Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724056
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at