3-43348090-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017719.5(SNRK):c.1831G>A(p.Gly611Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,588,962 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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 | UniProt |
---|---|---|---|---|---|---|---|
SNRK | NM_017719.5 | c.1831G>A | p.Gly611Ser | missense_variant | 7/7 | ENST00000296088.12 | |
SNRK-AS1 | NR_046757.1 | n.2304C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNRK | ENST00000296088.12 | c.1831G>A | p.Gly611Ser | missense_variant | 7/7 | 1 | NM_017719.5 | P1 | |
SNRK-AS1 | ENST00000607513.2 | n.823C>T | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000590 AC: 13AN: 220416Hom.: 0 AF XY: 0.0000583 AC XY: 7AN XY: 119976
GnomAD4 exome AF: 0.0000188 AC: 27AN: 1436682Hom.: 0 Cov.: 31 AF XY: 0.0000196 AC XY: 14AN XY: 712650
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.1831G>A (p.G611S) alteration is located in exon 7 (coding exon 5) of the SNRK gene. This alteration results from a G to A substitution at nucleotide position 1831, causing the glycine (G) at amino acid position 611 to be replaced by a serine (S). 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