chr3-43348156-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017719.5(SNRK):āc.1897A>Gā(p.Met633Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000259 in 1,583,040 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 Uncertain significance (ā ).
Frequency
Consequence
NM_017719.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNRK | NM_017719.5 | c.1897A>G | p.Met633Val | missense_variant | 7/7 | ENST00000296088.12 | NP_060189.3 | |
SNRK-AS1 | NR_046757.1 | n.2238T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNRK | ENST00000296088.12 | c.1897A>G | p.Met633Val | missense_variant | 7/7 | 1 | NM_017719.5 | ENSP00000296088 | P1 | |
SNRK-AS1 | ENST00000607513.2 | n.757T>C | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000500 AC: 11AN: 219956Hom.: 0 AF XY: 0.0000504 AC XY: 6AN XY: 119152
GnomAD4 exome AF: 0.0000259 AC: 37AN: 1430726Hom.: 0 Cov.: 31 AF XY: 0.0000324 AC XY: 23AN XY: 709366
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.1897A>G (p.M633V) alteration is located in exon 7 (coding exon 5) of the SNRK gene. This alteration results from a A to G substitution at nucleotide position 1897, causing the methionine (M) at amino acid position 633 to be replaced by a valine (V). 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