2-213489990-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024532.5(SPAG16):c.970C>A(p.Pro324Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00479 in 1,606,586 control chromosomes in the GnomAD database, including 311 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024532.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPAG16 | NM_024532.5 | c.970C>A | p.Pro324Thr | missense_variant | 10/16 | ENST00000331683.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPAG16 | ENST00000331683.10 | c.970C>A | p.Pro324Thr | missense_variant | 10/16 | 1 | NM_024532.5 | P1 | |
SPAG16 | ENST00000406979.6 | c.*971C>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/18 | 1 | ||||
SPAG16 | ENST00000451561.1 | c.28C>A | p.Pro10Thr | missense_variant | 1/6 | 3 | |||
SPAG16 | ENST00000452556.5 | c.*536C>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0249 AC: 3788AN: 152062Hom.: 155 Cov.: 32
GnomAD3 exomes AF: 0.00626 AC: 1532AN: 244590Hom.: 59 AF XY: 0.00467 AC XY: 618AN XY: 132454
GnomAD4 exome AF: 0.00267 AC: 3886AN: 1454406Hom.: 155 Cov.: 29 AF XY: 0.00233 AC XY: 1684AN XY: 723340
GnomAD4 genome AF: 0.0250 AC: 3803AN: 152180Hom.: 156 Cov.: 32 AF XY: 0.0243 AC XY: 1810AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at