chr11-72006255-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006185.4(NUMA1):c.5472T>A(p.Asp1824Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,018 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_006185.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUMA1 | NM_006185.4 | c.5472T>A | p.Asp1824Glu | missense_variant | 22/27 | ENST00000393695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUMA1 | ENST00000393695.8 | c.5472T>A | p.Asp1824Glu | missense_variant | 22/27 | 1 | NM_006185.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250552Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135544
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461702Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727160
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.5472T>A (p.D1824E) alteration is located in exon 22 (coding exon 20) of the NUMA1 gene. This alteration results from a T to A substitution at nucleotide position 5472, causing the aspartic acid (D) at amino acid position 1824 to be replaced by a glutamic acid (E). 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