chr11-72006221-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006185.4(NUMA1):c.5506T>C(p.Tyr1836His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0072 in 1,614,202 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006185.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUMA1 | NM_006185.4 | c.5506T>C | p.Tyr1836His | missense_variant | 22/27 | ENST00000393695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUMA1 | ENST00000393695.8 | c.5506T>C | p.Tyr1836His | missense_variant | 22/27 | 1 | NM_006185.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00567 AC: 863AN: 152210Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00539 AC: 1354AN: 251266Hom.: 10 AF XY: 0.00555 AC XY: 754AN XY: 135830
GnomAD4 exome AF: 0.00736 AC: 10756AN: 1461874Hom.: 59 Cov.: 31 AF XY: 0.00751 AC XY: 5463AN XY: 727244
GnomAD4 genome ? AF: 0.00566 AC: 862AN: 152328Hom.: 5 Cov.: 33 AF XY: 0.00514 AC XY: 383AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | NUMA1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at