19-45815688-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004819.3(SYMPK):āc.3697G>Cā(p.Ala1233Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,609,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004819.3 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 |
---|---|---|---|---|---|---|---|
SYMPK | NM_004819.3 | c.3697G>C | p.Ala1233Pro | missense_variant | 27/27 | ENST00000245934.12 | |
SYMPK | XM_011527354.2 | c.3697G>C | p.Ala1233Pro | missense_variant | 28/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYMPK | ENST00000245934.12 | c.3697G>C | p.Ala1233Pro | missense_variant | 27/27 | 1 | NM_004819.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152076Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000421 AC: 10AN: 237734Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130194
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1457458Hom.: 0 Cov.: 48 AF XY: 0.0000110 AC XY: 8AN XY: 724886
GnomAD4 genome AF: 0.000171 AC: 26AN: 152196Hom.: 0 Cov.: 28 AF XY: 0.000121 AC XY: 9AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.3697G>C (p.A1233P) alteration is located in exon 27 (coding exon 26) of the SYMPK gene. This alteration results from a G to C substitution at nucleotide position 3697, causing the alanine (A) at amino acid position 1233 to be replaced by a proline (P). 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